sknano.core.atoms.StructureAtom¶
-
class
sknano.core.atoms.
StructureAtom
(*args, *, NN=None, **kwargs)[source][source]¶ An
Atom
class for structure analysis.Parameters: element : {str, int}, optional
A string representation of the element symbol or an integer specifying an element atomic number.
id : int, optional
atom ID
mol : int, optional
molecule ID
type : int, optional
atom type
x, y, z : float, optional
x,y,z components of
StructureAtom
position vector relative to origin.vx, vy, vz : float, optional
vx,vy,vz components of
StructureAtom
velocity.Attributes
CN
StructureAtom
coordination number.NN
Nearest-neighbor Atoms
.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. first_neighbors
fmtstr
Format string. i
ix,iy,iz image flags id
id
.ix
ix image flag. iy
iy image flag. iz
iz image flag. lattice
Crystal3DLattice
.m
mass
Atomic mass ma in atomic mass units. mol
mol
.moleculeID
neighbor_distances
Neighbor atom distances. neighbors
Neighbor atoms. pbc
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 vectorvy
x component of VelocityAtom
velocity vectorvz
z component of VelocityAtom
velocity vectorx
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 byVector
t.