Resolve "Terminology: replace element with species"

Description

I systematically replaced instances of element with species (and sometimes chemical_symbols) throughout the Python code, wherever element was used in the sense of a chemical element (as opposed to an element of a vector). The changes are spread over the entire code but are very localized.

Comments

• One could still do something similar with the C++ code. The latter is, however, in any case subject of #60 (closed). Hence I excluded it from this MR (and issue).
• There are some minor adjustments of docstrings, which I made as I went through the code.
• I tried to adhere to the convention that species is used whenever one is dealing with a list of integers and chemical_symbols for list of strings. When ambiguous species was used.
• One exception: I kept inert_species in structure_mapping.py since inert_chemical_symbols would have become awkwardly long.

It would help to have another set of eyes to check this carefully, simply since there are a lot of places that are affected.

Closes #219 (closed)