sknano.core.atoms.XAtom

class sknano.core.atoms.XAtom(element=None, atomID=0, moleculeID=0, atomtype=1, q=0.0, m=None, mass=None, x=None, y=None, z=None, vx=None, vy=None, vz=None, fx=None, fy=None, fz=None, nx=None, ny=None, nz=None, **kwargs)

An Atom class with an eXtended set of attributes.

Parameters:

element : {str, int}, optional

A string representation of the element symbol or an integer specifying an element atomic number.

x, y, z : float, optional

\(x, y, z\) components of XAtom position vector relative to origin.

atomID : int, optional

atom ID

moleculeID : int, optional

molecule ID

atomtype : int, optional

atom type

q : {int, float}, optional

Net charge of XAtom.

vx, vy, vz : float, optional

\(v_x, v_y, v_z\) components of XAtom velocity.

nx, ny, nz : int, optional

\(n_x, n_y, n_z\) image flags

Attributes

Z	Atomic number \(Z\).
atomID	atomID.
atomtype	atomtype.
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.