doc: amended stuff and fixed hcp

Signed-off-by: Nick Papior <[email protected]>

Author: zerothi

sisl/geom/basic.py

@@ -97,10 +97,12 @@ def hcp(a, atom, coa=1.63333, orthogonal=False):
 
     Parameters
     ----------
-    alat : float
-        lattice parameter
+    a : float
+        lattice parameter for 1st and 2nd lattice vectors
     atom : Atom
         the atom in the HCP lattice
+    coa : float, optional
+        c over a parameter where c is the 3rd lattice vector length
     orthogonal : bool, optional
         whether the lattice is orthogonal (4 atoms)
     """

sisl/geom/bilayer.py

@@ -35,6 +35,11 @@ def bilayer(bond=1.42, bottom_atom=None, top_atom=None, stacking='AB',
     layer : {'both', 'bottom', 'top'}
        control which layer(s) to return
 
+    See Also
+    --------
+    honeycomb: honeycomb lattices
+    graphene: graphene geometry
+
     References
     ----------
     .. [1] G. Trambly de Laissardiere, D. Mayou, L. Magaud, "Localization of Dirac Electrons in Rotated Graphene Bilayers", Nano Letts. 10, 804-808 (2010)

sisl/geom/flat.py

@@ -22,6 +22,7 @@ def honeycomb(bond, atom, orthogonal=False):
     See Also
     --------
     graphene: the equivalent of this, but with default of Carbon atoms
+    bilayer: create bilayer honeycomb lattices
     """
     sq3h = 3.**.5 * 0.5
     if orthogonal:
@@ -59,6 +60,7 @@ def graphene(bond=1.42, atom=None, orthogonal=False):
     See Also
     --------
     honeycomb: the equivalent of this, but with non-default atoms
+    bilayer: create bilayer honeycomb lattices
     """
     if atom is None:
         return honeycomb(bond, Atom(Z=6, R=bond * 1.01), orthogonal)