From a6df54944a24f65e9543fd6991ce0b1c51207c81 Mon Sep 17 00:00:00 2001
From: Thomas Frederiksen <thomas_frederiksen@ehu.eus>
Date: Sat, 4 Nov 2023 13:12:26 +0100
Subject: [PATCH 01/15] enh: creation of chiral GNRs and [n]-triangulene

---
 CHANGELOG.md                |  2 +
 src/sisl/geom/flat.py       | 36 +++++++++++++--
 src/sisl/geom/nanoribbon.py | 87 +++++++++++++++++++++++++++++++------
 3 files changed, 109 insertions(+), 16 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 8ce2126f15..58e7d3bd4d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,6 +13,8 @@ we hit release version 1.0.0.
 ## [0.14.3] - 2023-11-07
 
 ### Added
+- 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`)
 - Creation of honeycomb flakes (`sisl.geom.honeycomb_flake`,
   `sisl.geom.graphene_flake`). #636
 - added `Geometry.as_supercell` to create the supercell structure,
diff --git a/src/sisl/geom/flat.py b/src/sisl/geom/flat.py
index 2610125048..05ef8e6950 100644
--- a/src/sisl/geom/flat.py
+++ b/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 +204,33 @@ 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) -> 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.
+    """
+    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:])
+    geom.cell[:2] *= (n + 4) / (n + 1)
+
+    # Center the molecule in cell
+    geom = geom.move([geom.cell[0, 0] - geom.xyz[-1, 0], 0, geom.cell[2, 2] / 2])
+
+    # Set boundary conditions
+    geometry_define_nsc(geom, [False, False, False])
+
+    return geom
diff --git a/src/sisl/geom/nanoribbon.py b/src/sisl/geom/nanoribbon.py
index 1543a386e9..0de0cec9e4 100644
--- a/src/sisl/geom/nanoribbon.py
+++ b/src/sisl/geom/nanoribbon.py
@@ -6,7 +6,7 @@
 
 import numpy as np
 
-from sisl import Atom, geom
+from sisl import Atom, Geometry, geom
 from sisl._internal import set_module
 
 from ._common import geometry_define_nsc
@@ -17,14 +17,17 @@
     "graphene_nanoribbon",
     "agnr",
     "zgnr",
+    "cgnr",
     "heteroribbon",
     "graphene_heteroribbon",
 ]
 
 
 @set_module("sisl.geom")
-def nanoribbon(width: int, bond: float, atoms, kind: str = "armchair"):
-    r"""Construction of a nanoribbon unit cell of type armchair or zigzag.
+def nanoribbon(
+    width: int, bond: float, atoms, kind: str = "armchair", index: (int, int) = (3, 1)
+) -> Geometry:
+    r"""Construction of a nanoribbon unit cell of type armchair, zigzag or (n,m)-chiral.
 
     The geometry is oriented along the :math:`x` axis.
 
@@ -36,8 +39,10 @@ def nanoribbon(width: int, bond: float, atoms, kind: str = "armchair"):
        bond length between atoms in the honeycomb lattice
     atoms : Atom
        atom (or atoms) in the honeycomb lattice
-    kind : {'armchair', 'zigzag'}
+    kind : {'armchair', 'zigzag', 'chiral'}
        type of ribbon
+    index :
+       chiral index (n, m), only processed for chiral types
 
     See Also
     --------
@@ -45,6 +50,7 @@ def nanoribbon(width: int, bond: float, atoms, kind: str = "armchair"):
     graphene : graphene geometry
     graphene_nanoribbon : graphene nanoribbon
     agnr : armchair graphene nanoribbon
+    cgnr : chiral graphene nanoribbon
     zgnr : zigzag graphene nanoribbon
     """
     if not isinstance(width, Integral):
@@ -65,7 +71,7 @@ def nanoribbon(width: int, bond: float, atoms, kind: str = "armchair"):
         else:
             ribbon = ribbon.repeat(n, 1)
 
-    elif kind == "zigzag":
+    elif kind in ["zigzag", "chiral"]:
         # Construct zigzag GNR
         ribbon = ribbon.rotate(90, [0, 0, -1], what="abc+xyz")
         if m == 1:
@@ -82,6 +88,23 @@ def nanoribbon(width: int, bond: float, atoms, kind: str = "armchair"):
         # Sort along x, then y
         ribbon = ribbon.sort(axis=(0, 1))
 
+        if kind == "chiral":
+            # continue with the zigzag ribbon as building block
+            n, m = index
+            ribbon = ribbon.tile(n + 1, 0)
+            r = ribbon.xyz[1] - ribbon.xyz[width]
+            ribbon.cell[0] += r + (m - 1) * (ribbon.xyz[2] - ribbon.xyz[0])
+            ribbon = ribbon.remove(range(width))
+            # determine rotation angle
+            x = ribbon.cell[0].copy()
+            x /= x.dot(x) ** 0.5
+            angle = np.arccos(x.dot([1, 0, 0]))
+            ribbon = ribbon.rotate(
+                angle, [0, 0, -1], origin=ribbon.xyz[0], rad=True, what="abc+xyz"
+            )
+            # set lattice vectors orthogonal
+            ribbon.cell[0, 1] = ribbon.cell[1, 0] = 0
+
     else:
         raise ValueError(f"nanoribbon: kind must be armchair or zigzag ({kind})")
 
@@ -98,8 +121,12 @@ def nanoribbon(width: int, bond: float, atoms, kind: str = "armchair"):
 
 @set_module("sisl.geom")
 def graphene_nanoribbon(
-    width: int, bond: float = 1.42, atoms=None, kind: str = "armchair"
-):
+    width: int,
+    bond: float = 1.42,
+    atoms=None,
+    kind: str = "armchair",
+    index: (int, int) = (3, 1),
+) -> Geometry:
     r"""Construction of a graphene nanoribbon
 
     Parameters
@@ -110,8 +137,10 @@ def graphene_nanoribbon(
        C-C bond length
     atoms : Atom, optional
        atom (or atoms) in the honeycomb lattice. Defaults to ``Atom(6)``
-    kind : {'armchair', 'zigzag'}
+    kind : {'armchair', 'zigzag', 'chiral}
        type of ribbon
+    index :
+       chiral index (n, m), only processed for chiral types
 
     See Also
     --------
@@ -120,14 +149,15 @@ def graphene_nanoribbon(
     nanoribbon : honeycomb nanoribbon (used for this method)
     agnr : armchair graphene nanoribbon
     zgnr : zigzag graphene nanoribbon
+    cgnr : chiral graphene nanoribbon
     """
     if atoms is None:
         atoms = Atom(Z=6, R=bond * 1.01)
-    return nanoribbon(width, bond, atoms, kind=kind)
+    return nanoribbon(width, bond, atoms, kind=kind, index=index)
 
 
 @set_module("sisl.geom")
-def agnr(width: int, bond: float = 1.42, atoms=None):
+def agnr(width: int, bond: float = 1.42, atoms=None) -> Geometry:
     r"""Construction of an armchair graphene nanoribbon
 
     Parameters
@@ -146,12 +176,13 @@ def agnr(width: int, bond: float = 1.42, atoms=None):
     nanoribbon : honeycomb nanoribbon
     graphene_nanoribbon : graphene nanoribbon
     zgnr : zigzag graphene nanoribbon
+    cgnr : chiral graphene nanoribbon
     """
     return graphene_nanoribbon(width, bond, atoms, kind="armchair")
 
 
 @set_module("sisl.geom")
-def zgnr(width: int, bond: float = 1.42, atoms=None):
+def zgnr(width: int, bond: float = 1.42, atoms=None) -> Geometry:
     r"""Construction of a zigzag graphene nanoribbon
 
     Parameters
@@ -170,10 +201,40 @@ def zgnr(width: int, bond: float = 1.42, atoms=None):
     nanoribbon : honeycomb nanoribbon
     graphene_nanoribbon : graphene nanoribbon
     agnr : armchair graphene nanoribbon
+    cgnr : chiral graphene nanoribbon
     """
     return graphene_nanoribbon(width, bond, atoms, kind="zigzag")
 
 
+@set_module("sisl.geom")
+def cgnr(n: int, m: int, width: int, bond: float = 1.42, atoms=None) -> Geometry:
+    r"""Construction of an (n, m, w)-chiral graphene nanoribbon
+
+    Parameters
+    ----------
+    n :
+       first chiral index
+    m :
+       second chiral index
+    width :
+       number of atoms in the transverse direction
+    bond :
+       C-C bond length
+    atoms : Atom, optional
+       atom (or atoms) in the honeycomb lattice. Defaults to ``Atom(6)``
+
+    See Also
+    --------
+    honeycomb : honeycomb lattices
+    graphene : graphene geometry
+    nanoribbon : honeycomb nanoribbon
+    graphene_nanoribbon : graphene nanoribbon
+    agnr : armchair graphene nanoribbon
+    zgnr : zigzag graphene nanoribbon
+    """
+    return graphene_nanoribbon(width, bond, atoms, kind="chiral", index=(n, m))
+
+
 @set_module("sisl.geom")
 @dataclass
 class _heteroribbon_section(CompositeGeometrySection):
@@ -638,7 +699,7 @@ def _parse_shift(self, shift, prev, align):
 
 
 @set_module("sisl.geom")
-def heteroribbon(sections, section_cls=_heteroribbon_section, **kwargs):
+def heteroribbon(sections, section_cls=_heteroribbon_section, **kwargs) -> Geometry:
     """Build a nanoribbon consisting of several nanoribbons of different widths.
 
     This function uses `composite_geometry`, but defaulting to the usage
@@ -688,7 +749,7 @@ def graphene_heteroribbon(
     bond: float = 1.42,
     atoms=None,
     **kwargs,
-):
+) -> Geometry:
     """Build a graphene nanoribbon consisting of several nanoribbons of different widths
 
     Please see `heteroribbon` for arguments, the only difference is that the `bond` and `atoms`

From 71ae22158cb55969d69ede113e6ce0f496e1b306 Mon Sep 17 00:00:00 2001
From: Thomas Frederiksen <thomas_frederiksen@ehu.eus>
Date: Sat, 4 Nov 2023 13:44:18 +0100
Subject: [PATCH 02/15] added tests for new geometries

---
 src/sisl/geom/tests/test_geom.py | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/src/sisl/geom/tests/test_geom.py b/src/sisl/geom/tests/test_geom.py
index 3112b55450..70cdab1637 100644
--- a/src/sisl/geom/tests/test_geom.py
+++ b/src/sisl/geom/tests/test_geom.py
@@ -74,6 +74,14 @@ def test_flat_flakes():
     )
 
 
+def test_triangulene():
+    g = triangulene(3)
+    assert g.na == 22
+    g = triangulene(3, atoms=["B", "N"])
+    assert g.atoms.nspecie == 2
+    g = triangulene(3, bond=1.6)
+
+
 def test_nanotube():
     a = nanotube(1.42)
     assert is_right_handed(a)
@@ -116,6 +124,8 @@ def test_nanoribbon():
     for w in range(0, 5):
         nanoribbon(w, 1.42, Atom(6), kind="armchair")
         nanoribbon(w, 1.42, Atom(6), kind="zigzag")
+        nanoribbon(w, 1.42, Atom(6), kind="chiral")
+        nanoribbon(w, 1.42, Atom(6), kind="chiral", index=(2, 2))
         nanoribbon(w, 1.42, (Atom(5), Atom(7)), kind="armchair")
         a = nanoribbon(w, 1.42, (Atom(5), Atom(7)), kind="zigzag")
         assert is_right_handed(a)
@@ -128,6 +138,9 @@ def test_nanoribbon():
 
 
 def test_graphene_nanoribbon():
+    graphene_nanoribbon(6, kind="armchair")
+    graphene_nanoribbon(6, kind="zigzag")
+    graphene_nanoribbon(6, kind="chiral")
     a = graphene_nanoribbon(5)
     assert is_right_handed(a)
 
@@ -142,6 +155,13 @@ def test_zgnr():
     assert is_right_handed(a)
 
 
+def test_cgnr():
+    a = cgnr(3, 1, 6)
+    a = cgnr(3, 1, 6, bond=1.6)
+    a = cgnr(3, 1, 6, atoms=["B", "N"])
+    assert is_right_handed(a)
+
+
 @pytest.mark.parametrize(
     "W, invert_first",
     itertools.product(range(3, 20), [True, False]),

From b3bf5724dc077478f01fa7eacae610dc467d80d0 Mon Sep 17 00:00:00 2001
From: Thomas Frederiksen <thomas_frederiksen@ehu.eus>
Date: Sat, 4 Nov 2023 13:48:05 +0100
Subject: [PATCH 03/15] doc: introduced 0D section and new geometries

---
 docs/api/default_geom.rst | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/docs/api/default_geom.rst b/docs/api/default_geom.rst
index c2436278e0..abd7c5427a 100644
--- a/docs/api/default_geom.rst
+++ b/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

From fc3d8e798f88016d29943f7bbd7cce60e479fe05 Mon Sep 17 00:00:00 2001
From: Thomas Frederiksen <thomas_frederiksen@ehu.eus>
Date: Sat, 4 Nov 2023 22:48:22 +0100
Subject: [PATCH 04/15] simple fixes

---
 src/sisl/geom/nanoribbon.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/sisl/geom/nanoribbon.py b/src/sisl/geom/nanoribbon.py
index 0de0cec9e4..964053bf8b 100644
--- a/src/sisl/geom/nanoribbon.py
+++ b/src/sisl/geom/nanoribbon.py
@@ -42,7 +42,7 @@ def nanoribbon(
     kind : {'armchair', 'zigzag', 'chiral'}
        type of ribbon
     index :
-       chiral index (n, m), only processed for chiral types
+       chiral index (n, m), only used if `kind=chiral`
 
     See Also
     --------
@@ -71,7 +71,7 @@ def nanoribbon(
         else:
             ribbon = ribbon.repeat(n, 1)
 
-    elif kind in ["zigzag", "chiral"]:
+    elif kind in ("zigzag", "chiral"):
         # Construct zigzag GNR
         ribbon = ribbon.rotate(90, [0, 0, -1], what="abc+xyz")
         if m == 1:
@@ -137,10 +137,10 @@ def graphene_nanoribbon(
        C-C bond length
     atoms : Atom, optional
        atom (or atoms) in the honeycomb lattice. Defaults to ``Atom(6)``
-    kind : {'armchair', 'zigzag', 'chiral}
+    kind : {'armchair', 'zigzag', 'chiral'}
        type of ribbon
     index :
-       chiral index (n, m), only processed for chiral types
+       chiral index (n, m), only used if `kind=chiral`
 
     See Also
     --------
@@ -213,9 +213,9 @@ def cgnr(n: int, m: int, width: int, bond: float = 1.42, atoms=None) -> Geometry
     Parameters
     ----------
     n :
-       first chiral index
+       first chirality index (zigzag segments)
     m :
-       second chiral index
+       second chirality index (armchair segments)
     width :
        number of atoms in the transverse direction
     bond :

From 8bcbe5566317fdb0a6c6c1fe66a358faf5ad26cc Mon Sep 17 00:00:00 2001
From: Thomas Frederiksen <thomas_frederiksen@ehu.eus>
Date: Sat, 4 Nov 2023 23:07:50 +0100
Subject: [PATCH 05/15] adopted chirality for the (n, m)-index

---
 src/sisl/geom/nanoribbon.py      | 23 ++++++++++++++---------
 src/sisl/geom/tests/test_geom.py |  2 +-
 2 files changed, 15 insertions(+), 10 deletions(-)

diff --git a/src/sisl/geom/nanoribbon.py b/src/sisl/geom/nanoribbon.py
index 964053bf8b..199057cb7d 100644
--- a/src/sisl/geom/nanoribbon.py
+++ b/src/sisl/geom/nanoribbon.py
@@ -3,6 +3,7 @@
 # file, You can obtain one at https://mozilla.org/MPL/2.0/.
 from dataclasses import dataclass, field
 from numbers import Integral
+from typing import Tuple
 
 import numpy as np
 
@@ -25,7 +26,11 @@
 
 @set_module("sisl.geom")
 def nanoribbon(
-    width: int, bond: float, atoms, kind: str = "armchair", index: (int, int) = (3, 1)
+    width: int,
+    bond: float,
+    atoms,
+    kind: str = "armchair",
+    chirality: Tuple[int, int] = (3, 1),
 ) -> Geometry:
     r"""Construction of a nanoribbon unit cell of type armchair, zigzag or (n,m)-chiral.
 
@@ -41,8 +46,8 @@ def nanoribbon(
        atom (or atoms) in the honeycomb lattice
     kind : {'armchair', 'zigzag', 'chiral'}
        type of ribbon
-    index :
-       chiral index (n, m), only used if `kind=chiral`
+    chirality :
+       index (n, m), only used if `kind=chiral`
 
     See Also
     --------
@@ -90,7 +95,7 @@ def nanoribbon(
 
         if kind == "chiral":
             # continue with the zigzag ribbon as building block
-            n, m = index
+            n, m = chirality
             ribbon = ribbon.tile(n + 1, 0)
             r = ribbon.xyz[1] - ribbon.xyz[width]
             ribbon.cell[0] += r + (m - 1) * (ribbon.xyz[2] - ribbon.xyz[0])
@@ -125,7 +130,7 @@ def graphene_nanoribbon(
     bond: float = 1.42,
     atoms=None,
     kind: str = "armchair",
-    index: (int, int) = (3, 1),
+    chirality: Tuple[int, int] = (3, 1),
 ) -> Geometry:
     r"""Construction of a graphene nanoribbon
 
@@ -139,8 +144,8 @@ def graphene_nanoribbon(
        atom (or atoms) in the honeycomb lattice. Defaults to ``Atom(6)``
     kind : {'armchair', 'zigzag', 'chiral'}
        type of ribbon
-    index :
-       chiral index (n, m), only used if `kind=chiral`
+    chirality :
+       index (n, m), only used if `kind=chiral`
 
     See Also
     --------
@@ -153,7 +158,7 @@ def graphene_nanoribbon(
     """
     if atoms is None:
         atoms = Atom(Z=6, R=bond * 1.01)
-    return nanoribbon(width, bond, atoms, kind=kind, index=index)
+    return nanoribbon(width, bond, atoms, kind=kind, chirality=chirality)
 
 
 @set_module("sisl.geom")
@@ -232,7 +237,7 @@ def cgnr(n: int, m: int, width: int, bond: float = 1.42, atoms=None) -> Geometry
     agnr : armchair graphene nanoribbon
     zgnr : zigzag graphene nanoribbon
     """
-    return graphene_nanoribbon(width, bond, atoms, kind="chiral", index=(n, m))
+    return graphene_nanoribbon(width, bond, atoms, kind="chiral", chirality=(n, m))
 
 
 @set_module("sisl.geom")
diff --git a/src/sisl/geom/tests/test_geom.py b/src/sisl/geom/tests/test_geom.py
index 70cdab1637..84e7d84f3b 100644
--- a/src/sisl/geom/tests/test_geom.py
+++ b/src/sisl/geom/tests/test_geom.py
@@ -125,7 +125,7 @@ def test_nanoribbon():
         nanoribbon(w, 1.42, Atom(6), kind="armchair")
         nanoribbon(w, 1.42, Atom(6), kind="zigzag")
         nanoribbon(w, 1.42, Atom(6), kind="chiral")
-        nanoribbon(w, 1.42, Atom(6), kind="chiral", index=(2, 2))
+        nanoribbon(w, 1.42, Atom(6), kind="chiral", chirality=(2, 2))
         nanoribbon(w, 1.42, (Atom(5), Atom(7)), kind="armchair")
         a = nanoribbon(w, 1.42, (Atom(5), Atom(7)), kind="zigzag")
         assert is_right_handed(a)

From aa21049daffca4d5809d6f7c83ce15711ce140ef Mon Sep 17 00:00:00 2001
From: Thomas Frederiksen <thomas_frederiksen@ehu.eus>
Date: Mon, 6 Nov 2023 22:02:27 +0100
Subject: [PATCH 06/15] redefined ribbon cell vectors and positioning in cells

---
 src/sisl/geom/nanoribbon.py | 29 ++++++++++++++++-------------
 1 file changed, 16 insertions(+), 13 deletions(-)

diff --git a/src/sisl/geom/nanoribbon.py b/src/sisl/geom/nanoribbon.py
index 199057cb7d..c9226701db 100644
--- a/src/sisl/geom/nanoribbon.py
+++ b/src/sisl/geom/nanoribbon.py
@@ -30,6 +30,7 @@ def nanoribbon(
     bond: float,
     atoms,
     kind: str = "armchair",
+    vacuum: float = 20.0,
     chirality: Tuple[int, int] = (3, 1),
 ) -> Geometry:
     r"""Construction of a nanoribbon unit cell of type armchair, zigzag or (n,m)-chiral.
@@ -46,6 +47,8 @@ def nanoribbon(
        atom (or atoms) in the honeycomb lattice
     kind : {'armchair', 'zigzag', 'chiral'}
        type of ribbon
+    vacuum :
+       separation in transverse direction
     chirality :
        index (n, m), only used if `kind=chiral`
 
@@ -75,6 +78,7 @@ def nanoribbon(
             ribbon = ribbon.remove(3 * (n + 1)).remove(0)
         else:
             ribbon = ribbon.repeat(n, 1)
+        ribbon.cell[1, 1] += vacuum
 
     elif kind in ("zigzag", "chiral"):
         # Construct zigzag GNR
@@ -86,9 +90,10 @@ def nanoribbon(
             ribbon = ribbon.tile(n, 0)
         # Invert y-coordinates
         ribbon.xyz[:, 1] *= -1
+
         # Set lattice vectors strictly orthogonal
         ribbon.cell[:, :] = np.diag(
-            [ribbon.cell[1, 0], -ribbon.cell[0, 1], ribbon.cell[2, 2]]
+            [ribbon.cell[1, 0], -ribbon.cell[0, 1] + vacuum, ribbon.cell[2, 2]]
         )
         # Sort along x, then y
         ribbon = ribbon.sort(axis=(0, 1))
@@ -101,27 +106,22 @@ def nanoribbon(
             ribbon.cell[0] += r + (m - 1) * (ribbon.xyz[2] - ribbon.xyz[0])
             ribbon = ribbon.remove(range(width))
             # determine rotation angle
-            x = ribbon.cell[0].copy()
-            x /= x.dot(x) ** 0.5
-            angle = np.arccos(x.dot([1, 0, 0]))
+            x = ribbon.cell[0]
+            angle = np.arccos(x.dot([1, 0, 0]) / x.dot(x) ** 0.5)
             ribbon = ribbon.rotate(
                 angle, [0, 0, -1], origin=ribbon.xyz[0], rad=True, what="abc+xyz"
             )
-            # set lattice vectors orthogonal
-            ribbon.cell[0, 1] = ribbon.cell[1, 0] = 0
+            # first lattice vector strictly along x
+            ribbon.cell[0, 1] = 0
 
     else:
         raise ValueError(f"nanoribbon: kind must be armchair or zigzag ({kind})")
 
-    # Separate ribbons along y-axis
-    ribbon.cell[1, 1] += 20.0
-
-    # Move inside unit cell
-    xyz = ribbon.xyz.min(axis=0) * [1, 1, 0]
-
     geometry_define_nsc(ribbon, [True, False, False])
 
-    return ribbon.move(-xyz + [0, 10, 0])
+    ribbon = ribbon.move(ribbon.center(what="cell") - ribbon.center())
+
+    return ribbon
 
 
 @set_module("sisl.geom")
@@ -130,6 +130,7 @@ def graphene_nanoribbon(
     bond: float = 1.42,
     atoms=None,
     kind: str = "armchair",
+    vacuum: float = 20.0,
     chirality: Tuple[int, int] = (3, 1),
 ) -> Geometry:
     r"""Construction of a graphene nanoribbon
@@ -144,6 +145,8 @@ def graphene_nanoribbon(
        atom (or atoms) in the honeycomb lattice. Defaults to ``Atom(6)``
     kind : {'armchair', 'zigzag', 'chiral'}
        type of ribbon
+    vacuum :
+       separation in transverse direction
     chirality :
        index (n, m), only used if `kind=chiral`
 

From 7746cf0f81ef440bdf8ff0f69c2e611bf2bd91d6 Mon Sep 17 00:00:00 2001
From: Thomas Frederiksen <thomas_frederiksen@ehu.eus>
Date: Mon, 6 Nov 2023 22:20:17 +0100
Subject: [PATCH 07/15] chirality index unified and vacuum argument introduced
 for all ribbons

---
 src/sisl/geom/nanoribbon.py | 35 ++++++++++++++++++++++++-----------
 1 file changed, 24 insertions(+), 11 deletions(-)

diff --git a/src/sisl/geom/nanoribbon.py b/src/sisl/geom/nanoribbon.py
index c9226701db..6c2b5e4b16 100644
--- a/src/sisl/geom/nanoribbon.py
+++ b/src/sisl/geom/nanoribbon.py
@@ -161,11 +161,11 @@ def graphene_nanoribbon(
     """
     if atoms is None:
         atoms = Atom(Z=6, R=bond * 1.01)
-    return nanoribbon(width, bond, atoms, kind=kind, chirality=chirality)
+    return nanoribbon(width, bond, atoms, kind=kind, vacuum=vacuum, chirality=chirality)
 
 
 @set_module("sisl.geom")
-def agnr(width: int, bond: float = 1.42, atoms=None) -> Geometry:
+def agnr(width: int, bond: float = 1.42, atoms=None, vacuum: float = 20.0) -> Geometry:
     r"""Construction of an armchair graphene nanoribbon
 
     Parameters
@@ -176,6 +176,8 @@ def agnr(width: int, bond: float = 1.42, atoms=None) -> Geometry:
        C-C bond length
     atoms : Atom, optional
        atom (or atoms) in the honeycomb lattice. Defaults to ``Atom(6)``
+    vacuum :
+       separation in transverse direction
 
     See Also
     --------
@@ -186,11 +188,11 @@ def agnr(width: int, bond: float = 1.42, atoms=None) -> Geometry:
     zgnr : zigzag graphene nanoribbon
     cgnr : chiral graphene nanoribbon
     """
-    return graphene_nanoribbon(width, bond, atoms, kind="armchair")
+    return graphene_nanoribbon(width, bond, atoms, kind="armchair", vacuum=vacuum)
 
 
 @set_module("sisl.geom")
-def zgnr(width: int, bond: float = 1.42, atoms=None) -> Geometry:
+def zgnr(width: int, bond: float = 1.42, atoms=None, vacuum: float = 20.0) -> Geometry:
     r"""Construction of a zigzag graphene nanoribbon
 
     Parameters
@@ -201,6 +203,9 @@ def zgnr(width: int, bond: float = 1.42, atoms=None) -> Geometry:
        C-C bond length
     atoms : Atom, optional
        atom (or atoms) in the honeycomb lattice. Defaults to ``Atom(6)``
+    vacuum :
+       separation in transverse direction
+
 
     See Also
     --------
@@ -211,25 +216,31 @@ def zgnr(width: int, bond: float = 1.42, atoms=None) -> Geometry:
     agnr : armchair graphene nanoribbon
     cgnr : chiral graphene nanoribbon
     """
-    return graphene_nanoribbon(width, bond, atoms, kind="zigzag")
+    return graphene_nanoribbon(width, bond, atoms, kind="zigzag", vacuum=vacuum)
 
 
 @set_module("sisl.geom")
-def cgnr(n: int, m: int, width: int, bond: float = 1.42, atoms=None) -> Geometry:
+def cgnr(
+    width: int,
+    chirality: Tuple[int, int],
+    bond: float = 1.42,
+    atoms=None,
+    vacuum: float = 20.0,
+) -> Geometry:
     r"""Construction of an (n, m, w)-chiral graphene nanoribbon
 
     Parameters
     ----------
-    n :
-       first chirality index (zigzag segments)
-    m :
-       second chirality index (armchair segments)
     width :
        number of atoms in the transverse direction
+    chirality :
+       index (n, m)
     bond :
        C-C bond length
     atoms : Atom, optional
        atom (or atoms) in the honeycomb lattice. Defaults to ``Atom(6)``
+    vacuum :
+       separation in transverse direction
 
     See Also
     --------
@@ -240,7 +251,9 @@ def cgnr(n: int, m: int, width: int, bond: float = 1.42, atoms=None) -> Geometry
     agnr : armchair graphene nanoribbon
     zgnr : zigzag graphene nanoribbon
     """
-    return graphene_nanoribbon(width, bond, atoms, kind="chiral", chirality=(n, m))
+    return graphene_nanoribbon(
+        width, bond, atoms, kind="chiral", vacuum=vacuum, chirality=chirality
+    )
 
 
 @set_module("sisl.geom")

From 1b47a5663916cf0a10dfb8aa3a12e85381b6f85e Mon Sep 17 00:00:00 2001
From: Thomas Frederiksen <thomas_frederiksen@ehu.eus>
Date: Mon, 6 Nov 2023 22:30:12 +0100
Subject: [PATCH 08/15] orthogonal cell for triangulene

---
 src/sisl/geom/flat.py | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/src/sisl/geom/flat.py b/src/sisl/geom/flat.py
index 05ef8e6950..89e48f4f84 100644
--- a/src/sisl/geom/flat.py
+++ b/src/sisl/geom/flat.py
@@ -207,7 +207,7 @@ def graphene_flake(
 
 
 @set_module("sisl.geom")
-def triangulene(n: int, bond: float = 1.42, atoms=None) -> Geometry:
+def triangulene(n: int, bond: float = 1.42, atoms=None, vacuum: float = 20.0) -> Geometry:
     """Construction of an [n]-triangulene geometry
 
     Parameters
@@ -219,16 +219,21 @@ def triangulene(n: int, bond: float = 1.42, atoms=None) -> Geometry:
     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:])
-    geom.cell[:2] *= (n + 4) / (n + 1)
+
+    # Set the cell according to the requested vacuum
+    size = np.max(geom.xyz[:], axis=0) - np.min(geom.xyz[:], axis=0)
+    geom.cell[:] = np.diag(size + vacuum)
 
     # Center the molecule in cell
-    geom = geom.move([geom.cell[0, 0] - geom.xyz[-1, 0], 0, geom.cell[2, 2] / 2])
+    geom = geom.move(geom.center(what="cell") - geom.center())
 
     # Set boundary conditions
     geometry_define_nsc(geom, [False, False, False])

From ca3275f5c9bfade8e8e129030683af7b8a1c3166 Mon Sep 17 00:00:00 2001
From: Thomas Frederiksen <thomas_frederiksen@ehu.eus>
Date: Mon, 6 Nov 2023 22:51:44 +0100
Subject: [PATCH 09/15] fix test_cgnr

---
 src/sisl/geom/tests/test_geom.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/sisl/geom/tests/test_geom.py b/src/sisl/geom/tests/test_geom.py
index 84e7d84f3b..01b5a4e75e 100644
--- a/src/sisl/geom/tests/test_geom.py
+++ b/src/sisl/geom/tests/test_geom.py
@@ -156,9 +156,9 @@ def test_zgnr():
 
 
 def test_cgnr():
-    a = cgnr(3, 1, 6)
-    a = cgnr(3, 1, 6, bond=1.6)
-    a = cgnr(3, 1, 6, atoms=["B", "N"])
+    cgnr(6, (3, 1), vacuum=0)
+    cgnr(6, (3, 1), bond=1.6)
+    a = cgnr(6, (3, 1), atoms=["B", "N"])
     assert is_right_handed(a)
 
 

From 65bffa69e6f036ead7adc63215b108e68aa8339d Mon Sep 17 00:00:00 2001
From: Thomas Frederiksen <thomas_frederiksen@ehu.eus>
Date: Mon, 6 Nov 2023 23:06:51 +0100
Subject: [PATCH 10/15] black fix

---
 src/sisl/geom/flat.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/sisl/geom/flat.py b/src/sisl/geom/flat.py
index 89e48f4f84..f9fafc4382 100644
--- a/src/sisl/geom/flat.py
+++ b/src/sisl/geom/flat.py
@@ -207,7 +207,9 @@ def graphene_flake(
 
 
 @set_module("sisl.geom")
-def triangulene(n: int, bond: float = 1.42, atoms=None, vacuum: float = 20.0) -> Geometry:
+def triangulene(
+    n: int, bond: float = 1.42, atoms=None, vacuum: float = 20.0
+) -> Geometry:
     """Construction of an [n]-triangulene geometry
 
     Parameters

From 493e20a5d095919d8e356f16590a445c6873621b Mon Sep 17 00:00:00 2001
From: Thomas Frederiksen <thomas_frederiksen@ehu.eus>
Date: Tue, 7 Nov 2023 11:41:31 +0100
Subject: [PATCH 11/15] minor fixes

---
 src/sisl/geom/flat.py       | 2 +-
 src/sisl/geom/nanoribbon.py | 6 ++++--
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/src/sisl/geom/flat.py b/src/sisl/geom/flat.py
index f9fafc4382..356b8e38e7 100644
--- a/src/sisl/geom/flat.py
+++ b/src/sisl/geom/flat.py
@@ -231,7 +231,7 @@ def triangulene(
     geom = geom.sub(idx[1:])
 
     # Set the cell according to the requested vacuum
-    size = np.max(geom.xyz[:], axis=0) - np.min(geom.xyz[:], axis=0)
+    size = geom.xyz.max(axis=0) - geom.xyz.min(axis=0)
     geom.cell[:] = np.diag(size + vacuum)
 
     # Center the molecule in cell
diff --git a/src/sisl/geom/nanoribbon.py b/src/sisl/geom/nanoribbon.py
index 6c2b5e4b16..d2cb0beb38 100644
--- a/src/sisl/geom/nanoribbon.py
+++ b/src/sisl/geom/nanoribbon.py
@@ -107,7 +107,9 @@ def nanoribbon(
             ribbon = ribbon.remove(range(width))
             # determine rotation angle
             x = ribbon.cell[0]
-            angle = np.arccos(x.dot([1, 0, 0]) / x.dot(x) ** 0.5)
+            angle = np.arccos(
+                x.dot([1, 0, 0]) / x.dot(x) ** 0.5
+            )  # angle of vectors, x and b=[1, 0, 0]
             ribbon = ribbon.rotate(
                 angle, [0, 0, -1], origin=ribbon.xyz[0], rad=True, what="abc+xyz"
             )
@@ -234,7 +236,7 @@ def cgnr(
     width :
        number of atoms in the transverse direction
     chirality :
-       index (n, m)
+       index (n, m) corresponding to an edge with n zigzag segments followed by m armchair segments
     bond :
        C-C bond length
     atoms : Atom, optional

From 8c16eaa0fd80dc1daf67ceb2212f052f89888265 Mon Sep 17 00:00:00 2001
From: Thomas Frederiksen <thomas_frederiksen@ehu.eus>
Date: Wed, 8 Nov 2023 11:44:58 +0100
Subject: [PATCH 12/15] nanoribbon atoms begin at zero along the first lattice
 vector (backwards compatibility)

---
 src/sisl/geom/nanoribbon.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/src/sisl/geom/nanoribbon.py b/src/sisl/geom/nanoribbon.py
index d2cb0beb38..eead8e4a2f 100644
--- a/src/sisl/geom/nanoribbon.py
+++ b/src/sisl/geom/nanoribbon.py
@@ -69,6 +69,7 @@ def nanoribbon(
     n, m = width // 2, width % 2
 
     ribbon = geom.honeycomb(bond, atoms, orthogonal=True)
+    angle = 0
 
     kind = kind.lower()
     if kind == "armchair":
@@ -121,8 +122,13 @@ def nanoribbon(
 
     geometry_define_nsc(ribbon, [True, False, False])
 
+    # move geometry into middle of the cell
     ribbon = ribbon.move(ribbon.center(what="cell") - ribbon.center())
 
+    # first atom to zero along the first lattice vector
+    x = ribbon.xyz[0]
+    ribbon = ribbon.move([x[1] * np.tan(angle) - x[0], 0, 0])
+
     return ribbon
 
 

From 77dae38dcc871be17a7f3d593b64b33398e11f75 Mon Sep 17 00:00:00 2001
From: Thomas Frederiksen <thomas_frederiksen@ehu.eus>
Date: Wed, 8 Nov 2023 14:36:26 +0100
Subject: [PATCH 13/15] vacuum as new parameter for heteroribbon

---
 src/sisl/geom/nanoribbon.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/src/sisl/geom/nanoribbon.py b/src/sisl/geom/nanoribbon.py
index eead8e4a2f..e3a8fa7ac9 100644
--- a/src/sisl/geom/nanoribbon.py
+++ b/src/sisl/geom/nanoribbon.py
@@ -322,6 +322,7 @@ class _heteroribbon_section(CompositeGeometrySection):
     atoms: Atom = None
     bond: float = None
     kind: str = "armchair"
+    vacuum: float = 20.0
     shift_quantum: bool = False
     on_lone_atom: str = field(default="ignore", repr=False)
     invert_first: bool = field(default=False, repr=False)
@@ -422,7 +423,7 @@ def _offset_from_center(self, align, prev):
 
     def build_section(self, prev):
         new_section = nanoribbon(
-            bond=self.bond, atoms=self.atoms, width=self.W, kind=self.kind
+            bond=self.bond, atoms=self.atoms, width=self.W, kind=self.kind, vacuum=self.vacuum,
         )
 
         align, offset = self._align_offset(prev, new_section)
@@ -511,7 +512,7 @@ def add_section(self, geom, new_section):
         new_min = new_section[:, self.trans_ax].min()
         new_max = new_section[:, self.trans_ax].max()
         if new_min < 0:
-            cell_offset = -new_min + 14
+            cell_offset = -new_min + self.vacuum
             geom = geom.add_vacuum(cell_offset, self.trans_ax)
             move = np.zeros(3)
             move[self.trans_ax] = cell_offset
@@ -519,7 +520,7 @@ def add_section(self, geom, new_section):
             new_section = new_section.move(move)
         if new_max > geom.cell[1, 1]:
             geom = geom.add_vacuum(
-                new_max - geom.cell[self.trans_ax, self.trans_ax] + 14, self.trans_ax
+                new_max - geom.cell[self.trans_ax, self.trans_ax] + self.vacuum, self.trans_ax
             )
 
         self.xyz = new_section.xyz

From e3482c5ffa610ada08643f356837c6286a84033e Mon Sep 17 00:00:00 2001
From: Thomas Frederiksen <thomas_frederiksen@ehu.eus>
Date: Wed, 8 Nov 2023 15:08:21 +0100
Subject: [PATCH 14/15] final polish after rebase

---
 CHANGELOG.md                | 9 +++++++--
 src/sisl/geom/nanoribbon.py | 9 +++++++--
 2 files changed, 14 insertions(+), 4 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 58e7d3bd4d..39fe2cda46 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,13 +8,18 @@ we hit release version 1.0.0.
 
 ## [0.14.4] - YYYY-MM-DD
 
+### Added
+- 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`)
+
+
+### Changed
+- `vacuum` is now an optional parameter for all ribbon structures
 
 
 ## [0.14.3] - 2023-11-07
 
 ### Added
-- 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`)
 - Creation of honeycomb flakes (`sisl.geom.honeycomb_flake`,
   `sisl.geom.graphene_flake`). #636
 - added `Geometry.as_supercell` to create the supercell structure,
diff --git a/src/sisl/geom/nanoribbon.py b/src/sisl/geom/nanoribbon.py
index e3a8fa7ac9..1bb95f2525 100644
--- a/src/sisl/geom/nanoribbon.py
+++ b/src/sisl/geom/nanoribbon.py
@@ -423,7 +423,11 @@ def _offset_from_center(self, align, prev):
 
     def build_section(self, prev):
         new_section = nanoribbon(
-            bond=self.bond, atoms=self.atoms, width=self.W, kind=self.kind, vacuum=self.vacuum,
+            bond=self.bond,
+            atoms=self.atoms,
+            width=self.W,
+            kind=self.kind,
+            vacuum=self.vacuum,
         )
 
         align, offset = self._align_offset(prev, new_section)
@@ -520,7 +524,8 @@ def add_section(self, geom, new_section):
             new_section = new_section.move(move)
         if new_max > geom.cell[1, 1]:
             geom = geom.add_vacuum(
-                new_max - geom.cell[self.trans_ax, self.trans_ax] + self.vacuum, self.trans_ax
+                new_max - geom.cell[self.trans_ax, self.trans_ax] + self.vacuum,
+                self.trans_ax,
             )
 
         self.xyz = new_section.xyz

From b741ac23be50b88a27fe1e38f75632586344915f Mon Sep 17 00:00:00 2001
From: Thomas Frederiksen <thomas_frederiksen@ehu.eus>
Date: Wed, 8 Nov 2023 15:32:56 +0100
Subject: [PATCH 15/15] added vacuum to docstring

---
 src/sisl/geom/nanoribbon.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/sisl/geom/nanoribbon.py b/src/sisl/geom/nanoribbon.py
index 1bb95f2525..2d6db6e2d4 100644
--- a/src/sisl/geom/nanoribbon.py
+++ b/src/sisl/geom/nanoribbon.py
@@ -294,6 +294,8 @@ class _heteroribbon_section(CompositeGeometrySection):
         The bond length of the ribbon.
     kind: {'armchair', 'zigzag'}
         The kind of ribbon that this section should be.
+    vacuum :
+        minimum separation in transverse direction
     shift_quantum: bool, optional
         Whether the implementation will assist avoiding lone atoms (< 2 neighbours).