MDAtom

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

Bases: sknano.core.atoms.energy_atoms.EnergyAtom, sknano.core.atoms.force_atoms.ForceAtom, sknano.core.atoms.velocity_atoms.VelocityAtom, sknano.core.atoms.structure_atoms.StructureAtom

An Atom sub-class for molecular dynamics trajectory analysis.

Parameters:reference_atom (Atom sub-class) –

Attributes

CN NeighborAtom coordination number.
NN Nearest-neighbor Atoms.
Nneighbors Number of neighbors.
POAV1 POAV1 instance.
POAV2 POAV2 instance.
POAVR POAVR instance.
Z Atomic number \(Z\).
angles Atom bond Angles.
atomID Alias for id.
atomtype
bonds Atom Bonds
dihedrals Atom Dihedrals
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 First nearest 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.
impropers Atom Impropers
ix \(i_x\) image flag.
iy \(i_y\) image flag.
iz \(i_z\) image flag.
ke Atom kinetic energy.
lattice Crystal3DLattice.
m An alias for mass.
mass Atomic mass \(m_a\) in atomic mass units.
mol mol.
moleculeID Alias for mol.
molid An alias for mol.
neighbor_distances Neighbor atom distances.
neighbor_map Neighbor atoms.
neighbors Neighbor atoms.
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.
reference_atom Reference atom.
reference_atom_bonds Return atom Bonds instance.
reference_atom_neighbors reference_atom neighbor atoms.
rs Scaled \(x, y, z\) components of Atom position vector.
second_neighbors Second nearest neighbors
serial Alias for id.
symbol Element symbol.
third_neighbors Third nearest neighbors
type type.
v \(v_x, v_y, v_z\) array of velocity components.
vmd_index VMD atom index attribute.
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.
xs Scaled \(x\)-coordinate.
y \(y\)-coordinate in units of Angstroms.
ys Scaled \(y\)-coordinate.
z \(z\)-coordinate in units of Angstroms.
zs Scaled \(z\)-coordinate.

Methods

get_coords([asdict]) Return atom coords.
get_nth_nearest_neighbors(n[, exclusive]) Get the `n`th set of neighbors.
getattr(attr[, default, recursive]) Get atom attribute named attr.
reset_attrs(**kwargs) Reset atom attributes.
rezero([epsilon]) Re-zero position vector components.
rezero_coords([epsilon]) Alias for Atom.rezero_xyz.
rezero_xyz([epsilon]) Re-zero position vector components.
rotate(**kwargs) Rotate Atom position vector.
set_nth_nearest_neighbors(n, neighbors) Set nth nearest neighbors
todict() Return dict of constructor parameters.
translate(t[, fix_anchor_point, cartesian]) Translate Atom position vector by Vector t.
update_attrs(**kwargs) Update atom attributes.

Attributes Summary

reference_atom Reference atom.
reference_atom_bonds Return atom Bonds instance.
reference_atom_neighbors reference_atom neighbor atoms.

Methods Summary

todict() Return dict of constructor parameters.

Attributes Documentation

reference_atom

Reference atom.

reference_atom_bonds

Return atom Bonds instance.

reference_atom_neighbors

reference_atom neighbor atoms.

Methods Documentation

todict()[source] [edit on github][source]

Return dict of constructor parameters.