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sknano.core.atoms.MDAtom

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

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 fx,fy,fz 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 ix,iy,iz image flags
id id.
ix ix image flag.
iy iy image flag.
iz iz image flag.
ke Atom kinetic energy.
lattice Crystal3DLattice.
m
mass Atomic mass ma 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 vx,vy,vz 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.