fixed lists and definition lists

Signed-off-by: Nick Papior <nickpapior@gmail.com>

Author: zerothi

docs/sisl_uses.bib

@@ -12,6 +12,7 @@ @ARTICLE{10.3389/fphy.2023.1237383
 ABSTRACT={Terahertz (THz) field pulses can now be applied in scanning tunneling microscopy (THz-STM) junction experiments to study time-resolved dynamics. The relatively slow pulse compared to the typical electronic time-scale calls for approximations based on a time-scale separation. Here, we contrast three methods based on non-equilibrium Green’s functions: i) the steady-state, adiabatic results, ii) the lowest-order dynamic expansion in the time variation, and iii) the auxiliary mode propagation method without approximations in the time variation. We consider a concrete THz-STM junction setup involving a hydrogen adsorbate on graphene where the localized spin polarization can be manipulated on/off by a local field from the tip electrode and/or a back-gate affecting the in-plane transport. We use steady-state non-equilibrium Green’s function theory combined with density functional theory to obtain a Hubbard model for the study of the junction dynamics. Solving the Hubbard model in a mean-field approximation, we find that the near-adiabatic first-order dynamic expansion in the time variation provides a good description for STM voltage pulses up to the 1 V range.}
 }
 
+
 @article{Brede2023,
  doi = {10.1038/s41467-023-42436-7}
 }

src/sisl/_core/_ufuncs_geometry.py

@@ -1484,10 +1484,13 @@ def scale(
        the scale factor for the new geometry (lattice vectors, coordinates
        and the atomic radii are scaled).
     what: {"abc", "xyz"}
+
        ``abc``
          Is applied on the corresponding lattice vector and the fractional coordinates.
+
        ``xyz``
          Is applied only to the atomic coordinates.
+
        If three different scale factors are provided, each will correspond to the
        Cartesian direction/lattice vector.
     scale_atoms :

src/sisl/_core/atom.py

@@ -997,9 +997,10 @@ class Atom(
     -----
     One can define atoms outside of the periodic table. They will generally
     be handled in this order:
-    - negative numbers will be converted into positive ones, and the returned
-      object will be an AtomGhost
-    - any other number (or name) not found in the periodic table will be returned
+
+    * negative numbers will be converted into positive ones, and the returned
+      object will be an `AtomGhost`
+    * any other number (or name) not found in the periodic table will be returned
       in an AtomUnknown object
 
     The mass for atoms outside the periodic table will default to 1e40 amu.

src/sisl/io/tbtrans/tbt.py

@@ -1021,7 +1021,7 @@ def fano(self, elec_from=0, elec_to=1, kavg=True, zero_T=1e-6) -> ndarray:
         .. math::
            F(E) &= \frac{\sum_{k,n} T_{k,n}(E)[1 - T_{k,n}(E)] w_k}{\sum_{k,n} T_{k,n}(E) w_k}
            \\
-                   &= S(E, V) / S_P(E, V)
+               &= S(E, V) / S_P(E, V)
 
         Notes
         -----
@@ -1035,7 +1035,7 @@ def fano(self, elec_from=0, elec_to=1, kavg=True, zero_T=1e-6) -> ndarray:
 
         For a spin-polarized calculation one should calculate the Fano factor as:
 
-            >>> up = get_sile('siesta.TBT_UP.nc')
+        >>> up = get_sile('siesta.TBT_UP.nc')
         >>> down = get_sile('siesta.TBT_DN.nc')
         >>> fano = up.fano() * up.transmission() + down.fano() * down.transmission()
         >>> fano /= up.transmission() + down.transmission()