Improve surface drawing so surface sites aren't drawn on top of adsorbates

[jonwzheng]

As noted in #2838 and elsewhere, surface drawing could be improved. In some cases the surface atoms are high up above the adsorbates, like:

I make the following suggestion:

Perhaps there can be improvements to coerce the orientation of the molecules if surface atoms are present (e.g. if surface atom z-index is high, then flip over)

Since there could be multiple surface atoms present, maybe this could only happen if >= 50% of the surface atoms are at least 50% higher between the lowest and highest atomic coordinates. (so a majority of surface points are higher than the middle, basically). If this happens, then flip the atom coordinates upside-down.