Metal improvements #16
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## master #16 +/- ##
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in some cases a seems to be far from the ASE reference
this should allow slab freezing that is agnostic to what atoms are present
on Li with the non-pbc fallback this tends to ruin lots of formerly not bad guesses
mostly copied from latest acat
…rprinting uses the site identity and morphology for each site and the xy distance and the signed z distance
before the translation was chosen first to keep the sites close to each other and then to keep them close to the center now for the second criteria instead of looking at the sites we look at the distances of the vertices of a box surrounding the adsorbate in xy fro the center
…nsion this greatly improves our ability to keep the adsorbates away from the edges
set_constraint clears prior constraints so it is important to only call it once with all desired constraints
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Adding a fix to run_harmonically_forced_xtb_no_pbc function. Needed to apply the new_constraints to the bigad atom object. Test shows adsorbate is now properly constrained.
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A few robustness improvement for dealing with other metals and adsorbates. Initial guess lattice parameter can be fed in rather than taken from ASE. Slab is frozen based on atom index rather than identify.