Atoms¶

This module creates the link between human-readable and computer-readable information about the studied system. Humans prefer to use string labels for molecules and atoms, whereas a computer only uses integers.

Atom type¶

An Atom instance is a representation of atomic information. Think of an Atom as a cell in an augmented periodic table. You can access the following fields :

name : the atom name;
symbol : the atom chemical type;
mass : the atom mass;
special::Dict{String, Any} : all the other values: charge, dipolar moment …;

The atom name and symbol may not be the same: if there are two kinds of hydrogen atoms in a simulation, they may have the names H1 and H2 ; and share the same symbol H.

Topology¶

A Topology instance stores all the information about the system : atomic types, atomic composition of the system, bonds, angles, dihedral agnles and molecules.

Atoms of the system can be accesed using integer indexing. The following example shows a few operations available on atoms:

# topology is a Topology with 10 atoms

atom = topology[3]  # Get a specific atom
println(atom.name)  # Get the atom name

atom.name = "H2"    # Set the atom name
topology[5] = atom  # Set the 5th atom of the topology

Topology functions¶

size(::Topology)¶: This function returns the number of atoms in the topology.

atomic_masses(::Topology)¶: This function returns a Vector{Float64} containing the masses of all the atoms in the system. If no mass was provided, it uses the ATOMIC_MASSES dictionnary to guess the values. If no value is found, the mass is set to \(0.0\). All the values are in internal units.

Periodic table information¶

The Atoms module also defines two dictonaries that store information about atoms:

ATOMIC_MASSES is a Dict{String, Float64} associating atoms symbols and atomic masses, in internal units ;
VDW_RADIUS is a Dict{String, Integer} associating atoms symbols and Van der Waals radii, in internal units.