diff --git a/aiidalab_widgets_base/viewers.py b/aiidalab_widgets_base/viewers.py index 744f1c3d9..18abdbf03 100644 --- a/aiidalab_widgets_base/viewers.py +++ b/aiidalab_widgets_base/viewers.py @@ -611,21 +611,21 @@ def compute_bonds(self, structure, radius=1.0, color="element", povray=False): cutoff = neighborlist.natural_cutoffs(structure, mult=1.09) bonds = [] + if len(structure) > 1: ii, jj, distances = neighborlist.neighbor_list( "ijD", structure, cutoff, self_interaction=False ) - for id1, id2, d_mic in zip(ii, jj, distances): + for id1, id2, bond_length in zip(ii, jj, distances): i = structure[id1] j = structure[id2] v1 = np.array([i.x, i.y, i.z]) - mic_vector = d_mic if povray: bond = vapory.Cylinder( v1, v1 - + mic_vector + + bond_length * Radius[i.symbol] / (Radius[i.symbol] + Radius[j.symbol]), 0.2, @@ -645,7 +645,7 @@ def compute_bonds(self, structure, radius=1.0, color="element", povray=False): tuple( ( v1 - + mic_vector + + bond_length * Radius[i.symbol] / (Radius[i.symbol] + Radius[j.symbol]) ).tolist()