added an as_supercell which returns geometry in supercell

CHANGELOG.md

@@ -8,6 +8,8 @@ we hit release version 1.0.0.
 ## [0.14.3] - YYYY-MM-DD
 
 ### Added
+- added `Geometry.as_supercell` to create the supercell structure,
+  thanks to @pfebrer for the suggestion
 - added `Lattice.to` and `Lattice.new` to function the same
   as `Geometry`, added Lattice.to["Cuboid"]
 - added `Atom.to`, currently only `to.Sphere()`

src/sisl/geometry.py

@@ -561,6 +561,46 @@ def as_primary(self, na_primary: int, axes=(0, 1, 2), ret_super: bool=False):
             return geom, supercell
         return geom
 
+    def as_supercell(self) -> Geometry:
+        """Create a new geometry equivalent to ``self * self.nsc``, where the indices are ordered as the supercells
+
+        Returns
+        -------
+        Geometry
+            the supercell expanded and reordered Geometry
+        """
+        # Get total number of atoms
+        na = len(self)
+        # create the big supercell geometry in the simplest (linear) way
+        sc = self * self.nsc
+
+        # remove nsc, this supercell should hold all information
+        sc.set_nsc([1, 1, 1])
+
+        # get off-set for first atom
+        # this is used to correct the indices created after having shifted
+        # everything
+        f0 = self.fxyz[0]
+
+        # translate the supercell such that the 0, 0, 0 (primary cell)
+        # is located at the origin.
+        sc = sc.translate(-(self.nsc // 2) @ self.cell)
+
+        # Calculate the translation table such that the ordering in `sc` can
+        # be made to look like the `self` supercell indices
+        isc_sc = np.rint(sc.xyz[::na] @ self.icell.T - f0).astype(np.int32)
+        isc_self = self.a2isc(np.arange(self.n_s) * na)
+        def new_sub(isc):
+            return (abs(isc_sc - isc).sum(1) == 0).nonzero()[0][0]
+
+        # Create the translation table for the indices
+        translate = np.array([new_sub(isc) for isc in isc_self])
+        # make sure all atoms are present
+        translate = np.repeat(translate * na, na).reshape(-1, na) + np.arange(na)
+
+        # re-arrange the atoms and return
+        return sc.sub(translate.ravel())
+
     def reorder(self) -> None:
         """ Reorders atoms according to first occurence in the geometry
 

src/sisl/tests/test_geometry.py

@@ -1738,6 +1738,20 @@ def test_translate2uc_axes():
     assert np.allclose(gr_once.xyz, gr_individual.xyz)
 
 
+def test_as_supercell_graphene():
+    gr = sisl_geom.graphene()
+    grsc = gr.as_supercell()
+    assert np.allclose(grsc.xyz[:len(gr)], gr.xyz)
+    assert np.allclose(grsc.axyz(np.arange(gr.na_s)), gr.axyz(np.arange(gr.na_s)))
+
+
+def test_as_supercell_fcc():
+    g = sisl_geom.fcc(2 ** 0.5, Atom(1, R=1.0001))
+    gsc = g.as_supercell()
+    assert np.allclose(gsc.xyz[:len(g)], g.xyz)
+    assert np.allclose(gsc.axyz(np.arange(g.na_s)), g.axyz(np.arange(g.na_s)))
+
+
 def test_sc_warn():
     with pytest.warns(SislDeprecation):
         lattice = sisl_geom.graphene().sc