Chemspecies update

[tjjarvinen]

This is update to ChemicalSpecies.

• Change info field to name field and make it represent 4 characters
• Add function atomic_name to access the new name field if given, else return atomic_symbol
• Added masses for isotopes
• Added symbol X to valid input. Gives weightless particle with atomic number zero

The idea with atomic_name is to represent PDB file format defines atom name columns (13-16). While element_symbol represents element columns (77-78)

1. element_symbol always gives the symbol of the element
2. atomic_symbol adds isotope information if given
3. atomic_name defaults to atomic_symbol, but overwrites it with atomic_name if species has that information.

This works now

julia> ChemicalSpecies(:C)
C

julia> ChemicalSpecies(:C12)
C12

julia> ChemicalSpecies(:C; atomic_name=:MyC)
C

julia> ChemicalSpecies(:C13; atomic_name=:MyC)
C13

julia> ChemicalSpecies(:X)
X

Comparisons

The basic idea is that if no isotope or name information is given, then that ChemicalSpecies works as a general atom with that atomic number.

atomic_name on the other hand is used to distinguish atoms with same type of atoms.

# true
ChemicalSpecies(:C13) == ChemicalSpecies(:C)

# false
ChemicalSpecies(:C12) == ChemicalSpecies(:C13)

# true
ChemicalSpecies(:C; atomic_name=:MyC) == ChemicalSpecies(:C)

# true
ChemicalSpecies(:C12; atomic_name=:MyC) == ChemicalSpecies(:C12)

# false
ChemicalSpecies(:C; atomic_name=:MyC) == ChemicalSpecies(:C12)

# true
ChemicalSpecies(:C12; atomic_name=:MyC) == ChemicalSpecies(:C)

# true
ChemicalSpecies(:C; atomic_name=:MyC) == ChemicalSpecies(:C12; atomic_name=:MyC)

So basically, you can create a potential using ChemicalSpecies(:C). Users can then mark their systems with isotopes or atomic names, for some additional information and the potential that uses "the general carbon" works with them.

masses

julia> mass(ChemicalSpecies(:C))
12.011 u

julia> mass(ChemicalSpecies(:C12))
12.0 u

julia> mass(ChemicalSpecies(:C13))
13.003354835340001 u

julia> mass(ChemicalSpecies(:C; atomic_name=:MyC))
12.011 u

julia> mass(ChemicalSpecies(:C13; atomic_name=:MyC))
13.003354835340001 u

julia> mass(ChemicalSpecies(:X))
0.0 u

@mfherbst @cortner

[rashidrafeek]

just a suggestion: atomic_name seems to imply the name is a property of the atom itself instead of an identifier (which seems to be the case here). Wouldn't just atom_name be better which also matches the PDB defintion?