MDAtom

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

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()

Return dict of constructor parameters.