Class representations of nature’s building blocks (sknano.core.atoms)


The Atom class represents a single atom. The Atoms class is a container class for Atom class instances. Sub-classes of Atom classes add new atom attributes to the Atom class. Every Atom sub-class has a corresponding container class that sub-classes the Atoms class.

Base Atom/Atoms classes

Atom(*args, *[, element, mass, Z]) Base class for abstract representation of structure atom.
Atoms([atoms, casttype]) Base class for collection of Atom objects.

Atom/Atoms sub-classes

ChargedAtom(*args, *[, q]) An Atom class with an electric charge attribute.
ChargedAtoms([atoms, casttype]) An Atoms sub-class for ChargedAtoms.
CNAtom(*args, *[, CN]) An Atom class with a coordination number attribute.
CNAtoms([atoms, casttype]) An Atoms sub-class for CNAtoms.
DipoleAtom(*args, *[, px, py, pz]) An Atom class with electric dipole moment attributes.
DipoleAtoms([atoms, casttype]) An Atoms sub-class for DipoleAtoms.
EnergyAtom(*args, *[, pe, ke, etotal]) An Atom class with energy attributes.
EnergyAtoms([atoms, casttype]) An Atoms sub-class for EnergyAtoms.
ForceAtom(*args, *[, fx, fy, fz]) An Atom class with force attributes.
ForceAtoms([atoms, casttype]) An Atoms sub-class for ForceAtoms.
IDAtom(*args, *[, id, mol]) An Atom class with id attributes.
IDAtoms([atoms, casttype]) An Atoms sub-class for IDAtoms.
ImageAtom(*args, *[, ix, iy, iz]) An Atom sub-class with image count attributes.
ImageAtoms([atoms, casttype]) An Atoms sub-class for ImageAtoms.
LatticeAtom(*args, *[, lattice, xs, ys, zs]) Class representation of a crystal structure lattice atom.
LatticeAtoms([atoms, casttype]) An Atoms sub-class for crystal structure lattice atoms.
PBCAtom(*args, *[, xperiodic, yperiodic, ...]) Atom class with PBC attributes.
PBCAtoms([atoms, casttype]) Atoms class for PBC.
TypeAtom(*args, *[, type]) An Atom class with an atom type attribute.
TypeAtoms([atoms]) An Atoms sub-class for TypeAtoms.
VanDerWaalsAtom(*args, *[, r_vdw]) An Atom class with a van der Waals radius attribute.
VanDerWaalsAtoms([atoms, casttype]) An Atoms sub-class for VanDerWaalsAtoms.
VelocityAtom(*args, *[, vx, vy, vz]) An Atom class with velocity component attributes.
VelocityAtoms([atoms, casttype]) An Atoms class for VelocityAtoms.
XYZAtom(*args, *[, x, y, z]) An Atom class with x, y, z attributes.
XYZAtoms([atoms, casttype]) An Atoms sub-class for XYZAtoms.

Mixin Atom/Atoms classes

KDTreeAtomMixin Mixin Atom class for KDTree analysis.
KDTreeAtomsMixin Mixin Atoms class for KDTree analysis.
NeighborAtomMixin Mixin class for neighbor analysis.
NeighborAtomsMixin Mixin Atoms class for NN analysis.
POAVAtomMixin Mixin class for POAV analysis.
POAVAtomsMixin Mixin class for POAV analysis.
POAV(sigma_bonds) Base class for POAV analysis.
POAV1(*args) POAV sub-class for POAV1 analysis.
POAV2(*args) POAV sub-class for POAV2 analysis.
POAVR(*args) POAV sub-class for POAVR analysis.

Combined sub-classes

BasisAtom(*args, *[, xperiodic, yperiodic, ...]) An abstract object representation of a crystal structure basis atom.
BasisAtoms([atoms, casttype]) An Atoms sub-class for crystal structure basis atoms.
MDAtom(*args, *[, reference_atom, t0_atom]) An Atom class for molecular dynamics trajectory analysis.
MDAtoms([atoms, kNN, NNrc]) An Atoms sub-class for molecular dynamics trajectory analysis.
StructureAtom(*args, *[, NN]) An Atom class for structure analysis.
StructureAtoms([atoms, kNN, NNrc]) An Atoms sub-class for structure analysis.

Bond/Bonds classes

Bond(atom1, atom2) Abstract representation of bond between 2 Atom objects.
Bonds([bonds]) Base class for collection of atom Bonds.

Classes for molecular dynamics simulations

Trajectory([snapshots]) Base class for trajectory analysis.
Snapshot([trajectory]) Container class for Trajectory data at single timestep