otherwise issues can occur with constraints during the structure comparison

…acat explicitly

…e occupied sites

…D repr

note RMG has a function for doing this, but it is too slow for the graphs including all surface sites

…nerate an electronic representation of molecule

this is mostly to faciliate visualization of sites

…cts from TS

…ite identities) a particular adsorbate can have

Enable T boltzmann weighted contributions to the weight vector
reloop the greedy optimization to improve convergence to local minimum
fix NaN related bugs

…cting configurations to calculate

This helps ensure the the only long path in the decomposition is between the two target adsorbates, but still provides room around each target adsorbate to enable accounting for many body interactions

enforces strict N_nodes = node_fract_training*N_training_points

since ontop sites are higher above the lattice than bridge and hollow sites the bond length can be a bit longer.
important for vdW species as well like NH3*

lets fix_bond_orders be passed flags causing it to preserve vdW for bonds that connect an otherwise gas-phase species to the surface and to include all vdW surface bonds

…at use fix_bond_orders