Atoms

The Atoms object represents a collection of atoms. It is used to store the positions, symbols, and other properties of the atoms. The sytax is very similar to ASE Atoms object. However, there are also some key differences regarding the species and attributes.

Example:

const myAtoms = new Atoms({
    symbols: ['O', 'H', 'H'], // symbols of the atoms
    positions: [[5, 5, 5], [6, 5, 5], [4, 5, 5]] // Positions of the atoms
    cell: [[10, 0, 0], [0, 10, 0], [0, 0, 10]], // Defining a cubic unit cell
    pbc: [true, true, true], // Periodic boundary conditions in all directions
});

In this example, an Atoms object is created to represent a water molecule within a cubic unit cell with periodic boundaries. The object includes definitions for the symbols, positions of the atoms.

Specie

Why do we use species instead of elements? Because of we want to store different properties for the same element:

• such as: colors, bonds, etc.

• In DFT calculation, different potentials, basis sets, charge, magnetic moment, etc.

A specie has:

• symbol: the name of the specie, e.g. ‘O’, ‘H1’, ‘Fe_up’, etc.

• element: the element symbol, e.g. ‘O’, ‘H’, ‘Fe’, etc.

• number: the atomic number of the element, e.g. 8, 1, 26, etc.

One can define the species explicitly using the species attribute.

const myAtoms = new Atoms({
    symbols: ['O', 'H1', 'H2'], // symbols of the atoms
    species: {'H1': 'H', 'H2': 'H'}, // Defining the species
});

Attributes and domain

One can store additional data in the Atoms object using the attributes. The attributes has two domains:

• atom: store data that is specific to each atom, such as the charge or force.

• specie: store data that is specific to each specie, such as the mass, color, or radius.

attributes: {'atom': {'charge': [0, 0, 0],
                        'force': [[0, 0, 0], [0, 0, 0], [0, 0, 0]],
                        },
            'specie': {'mass': {'O': 15.999, 'H': 1.008},
                        "color", {C: "red", H: "#b434eb", O: "#34eb77", S: "#FFFF00" },
                        "radius", {C: 0.77, H: 0.37, O: 0.66, S: 1.04},
                        },
            }

Methods

The Atoms object has a number of methods that can be used to manipulate the data. These include methods to:

Atomic and Specie Manipulation

• addSpecie(symbol, element = null)

• addAtom(atom)

• replaceAtoms(indices, newSpecieSymbol)

Cell and Boundary Conditions

• setCell(cell)

• setPBC(pbc)

Attributes and Properties

• newAttribute(name, values, domain = “atom”)

• getAttribute(name, domain = “atom”)

Geometric Transformations

• translate(t)

• rotate(axis, angle, rotate_cell = false)

• center(vacuum = 0.0, axis = [0, 1, 2], center = null)

Advanced Manipulations

• multiply(mx, my, mz)

• deleteAtoms(indices)

Information and Export

• getAtomsCount()

• getSpeciesCount()

• getCellLengthsAndAngles()

• calculateFractionalCoordinates()

• toDict()

• copy()

• getCenterOfGeometry()

• getAtomsByIndices(indices)