I'm using SOAP descriptors for predicting a property for atomic environments. I have a "dummy" species A present in some environments, which in principle has the same atomic number as another species B, but the interaction between A and B is defined according to different rules. So SOAP should be able to differentiate between A and B.

What atomic number should be assigned to the species A in this case? It cannot be the same as B, as the difference will be lost when constructing the descriptor. It seems like atomic number zero is treated somehow specifically as a "wild-card", so it doesn't look like a safe option. Assigning an arbitrary atomic number between 1 and 118 might work, but it will be annoying if that specific atomic number happens to appear in another system later. Assigning atomic number -1 seems to work and produce the same descriptor as assigning atomic number between 1 and 118 not equal to B's atomic number (but different from assigning zero...), but I'm worried this is due to unreliable behavior of reading an array out of bounds somewhere.