sknano.core.atoms.MDAtom

class sknano.core.atoms.MDAtom(*args, *, reference_atom=None, t0_atom=None, **kwargs)

An Atom class for molecular dynamics trajectory analysis.

Attributes

CN	StructureAtom coordination number.
NN
POAV1	POAV1 instance.
POAV2	POAV2 instance.
POAVR	POAVR instance.
Z	Atomic number \(Z\).
atomID
atomtype
bonds	Return atom Bonds instance.
dr	\(x, y, z\) components of Atom displacement vector.
element	Element symbol.
etotal	Atom total energy (pe + ke).
f	\(f_x, f_y, f_z\) array of force vector components.
first_neighbors
fmtstr	Format string.
fx	\(x\) component of ForceAtom force vector
fy	\(x\) component of ForceAtom force vector
fz	\(z\) component of ForceAtom force vector
i	\(i_x, i_y, i_z\) image flags
id	id.
ix	\(i_x\) image flag.
iy	\(i_y\) image flag.
iz	\(i_z\) image flag.
ke	Atom kinetic energy.
lattice	Crystal3DLattice.
m
mass	Atomic mass \(m_a\) in atomic mass units.
mol	mol.
moleculeID
neighbor_distances	Neighbor atom distances.
neighbors	Neighbor atoms.
pbc
pe	Atom potential energy.
q	Charge \(q\) as multiple of elementary charge \(e\).
r	\(x, y, z\) components of Atom position vector.
r0	\(x, y, z\) components of Atom position vector at t=0.
rs	\(x, y, z\) components of Atom position vector.
second_neighbors
symbol	Element symbol.
third_neighbors
type	type.
v	\(v_x, v_y, v_z\) array of velocity components.
vx	\(x\) component of VelocityAtom velocity vector
vy	\(x\) component of VelocityAtom velocity vector
vz	\(z\) component of VelocityAtom velocity vector
x	\(x\)-coordinate in units of Angstroms.
xperiodic
xs	\(x\)-coordinate in units of Angstroms.
y	\(y\)-coordinate in units of Angstroms.
yperiodic
ys	\(y\)-coordinate in units of Angstroms.
z	\(z\)-coordinate in units of Angstroms.
zperiodic
zs	\(z\)-coordinate in units of Angstroms.

Methods

get_coords([asdict])	Return atom coords.
get_neighbors(n)
rezero([epsilon])	Re-zero velocity vector components.
rezero_coords([epsilon])	Alias for Atom.rezero_xyz.
rezero_xyz([epsilon])	Re-zero position vector components.
rotate(**kwargs)	Rotate Atom velocity vector.
set_neighbors(n, neighbors)
todict()
translate(t[, fix_anchor_point])	Translate Atom position vector by Vector t.