Atoms

Atoms(parent)

Bases: Container

Information that specifies atoms.

atomic_numbers = Data[adt.UInt8](store_kind=(StoreKind.ARRAY), uuid='d051abd9-c815-40b1-ab2d-e7a50a2d3259', description='Atomic numbers')

The atomic number is a fundamental property of an atom and is denoted by the symbol \(Z\). It is defined as the number of protons in the nucleus of an atom. In a neutral atom, the atomic number also corresponds to the number of electrons orbiting the nucleus.

cadence = Cadence.ENSEMBLE

label = 'atoms'

symbols = Data[adt.Str](store_kind=(StoreKind.ARRAY), uuid='81c21a83-4b72-48c6-a576-4541b468eb90', description='Elemental symbols')

Elemental symbol based on [atom_z][containers.atomistic.microstate.Microstates.atom_z].

types = Data[adt.Str](store_kind=(StoreKind.ARRAY), uuid='e34c0e1b-0eaa-4679-b060-3fcfe737aa15', description='Classical force field atom type')

In the context of force fields used in molecular dynamics simulations, an "atom type" refers to a specific classification assigned to individual atoms within a molecular system based on certain characteristics. Atom types play a crucial role in defining the parameters and potential energy functions used to calculate forces and motions during a simulation.

Each atom in a molecular system is assigned a particular atom type, which is typically associated with a set of parameters defining its behavior. These parameters include values such as atomic mass, partial charges, van der Waals radii, and bond, angle, and dihedral force constants. The specific values for these parameters are determined based on experimental data and quantum mechanical calculations.

n_atoms(view=None, run_id=None)

Total number of atoms in this ensemble.