sknano.core.atoms.KDTAtom

class sknano.core.atoms.KDTAtom(CN=0, NN=None, bonds=None, **kwargs)

An Atom class for KDTree analysis.

Parameters:

CN : int, optional

KDTAtom coordination number.

NN : {sequence, Atoms}, optional

List of nearest-neighbor Atoms

bonds : {sequence, Bonds}, optional

List of atom Bonds or Bonds instance

Attributes

CN	Return KDTAtom coordination number.
NN	Nearest-neighbor Atoms.
Z	Atomic number \(Z\).
atomID	atomID.
atomtype	atomtype.
bonds	Return atom Bonds instance.
dr	\(x, y, z\) components of Atom displacement vector.
element	Element symbol.
f	\(f_x, f_y, f_z\) array of force vector components.
fx	\(x\) component of XAtom force vector
fy	\(x\) component of XAtom force vector
fz	\(z\) component of XAtom force vector
m	Atomic mass \(m_a\) in atomic mass units.
mass
moleculeID	moleculeID.
n	\(n_x, n_y, n_z\) image flags of XAtom.
nx	\(n_x\) image flag.
ny	\(n_y\) image flag.
nz	\(n_z\) image flag.
q	Charge \(q\) as multiple of elementary charge \(e\).
r	\(x, y, z\) components of Atom position vector.
symbol	Element symbol.
v	\(v_x, v_y, v_z\) array of velocity components.
vx	\(x\) component of XAtom velocity vector
vy	\(x\) component of XAtom velocity vector
vz	\(z\) component of XAtom velocity vector
x	\(x\)-coordinate in units of Angstroms.
y	\(y\)-coordinate in units of Angstroms.
z	\(z\)-coordinate in units of Angstroms.

Methods

get_coords([asdict])	Return atom coords.
rezero([epsilon])	Re-zero position vector components.
rezero_coords([epsilon])	Alias for Atom.rezero.
rotate([angle, rot_axis, anchor_point, ...])	Rotate Atom position vector.
todict()
translate(t[, fix_anchor_point])	Translate Atom position vector by Vector t.