XYZAtom¶
-
class
sknano.core.atoms.
XYZAtom
(*args, x=None, y=None, z=None, **kwargs)[source] [edit on github][source]¶ Bases:
sknano.core.atoms.atoms.Atom
An
Atom
sub-class with x, y, z attributes.Parameters: - element ({str, int}, optional) – A string representation of the element symbol or an integer specifying an element atomic number.
- y, z (x,) – x,y,z components of
XYZAtom
position vector relative to origin.
Attributes
Z
Atomic number Z. dr
x,y,z components of Atom
displacement vector.element
Element symbol. fmtstr
Format string. m
An alias for mass
.mass
Atomic mass ma in atomic mass units. r
x,y,z components of Atom
position vector.r0
x,y,z components of Atom
position vector at t=0.symbol
Element symbol. 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. getattr
(attr[, default, recursive])Get atom attribute named attr
.reset_attrs
(**kwargs)Reset atom attributes. rezero
([epsilon])Alias for Atom.rezero_xyz
, but callssuper
classrezero
method as well.rezero_coords
([epsilon])Alias for Atom.rezero_xyz
.rezero_xyz
([epsilon])Re-zero position vector components. todict
()Return dict
of constructor parameters.update_attrs
(**kwargs)Update atom attributes. Attributes Summary
dr
x,y,z components of Atom
displacement vector.r
x,y,z components of Atom
position vector.r0
x,y,z components of Atom
position vector at t=0.x
x-coordinate in units of Angstroms. y
y-coordinate in units of Angstroms. z
z-coordinate in units of Angstroms. Methods Summary
get_coords
([asdict])Return atom coords. rezero
([epsilon])Alias for Atom.rezero_xyz
, but callssuper
classrezero
method as well.rezero_coords
([epsilon])Alias for Atom.rezero_xyz
.rezero_xyz
([epsilon])Re-zero position vector components. todict
()Return dict
of constructor parameters.Attributes Documentation
-
dr
¶ x,y,z components of
Atom
displacement vector.Returns: 3-element ndarray of [x,y,z] coordinates of Atom
.Return type: ndarray
-
r
¶ x,y,z components of
Atom
position vector.Returns: 3D Vector
of [x,y,z] coordinates ofAtom
.Return type: Vector
-
r0
¶ x,y,z components of
Atom
position vector at t=0.Returns: 3-element ndarray of [x,y,z] coordinates of Atom
.Return type: ndarray
-
x
¶ x-coordinate in units of Angstroms.
Returns: x-coordinate in units of Angstroms. Return type: float
-
y
¶ y-coordinate in units of Angstroms.
Returns: y-coordinate in units of Angstroms. Return type: float
-
z
¶ z-coordinate in units of Angstroms.
Returns: z-coordinate in units of Angstroms. Return type: float
Methods Documentation
-
get_coords
(asdict=False)[source] [edit on github][source]¶ Return atom coords.
Parameters: asdict (bool, optional) – Returns: coords Return type: OrderedDict
or ndarray
-
rezero
(epsilon=1e-10)[source] [edit on github][source]¶ Alias for
Atom.rezero_xyz
, but callssuper
classrezero
method as well.
-
rezero_coords
(epsilon=1e-10)[source] [edit on github][source]¶ Alias for
Atom.rezero_xyz
.
-
rezero_xyz
(epsilon=1e-10)[source] [edit on github][source]¶ Re-zero position vector components.
Set position vector components with absolute value less than
epsilon
to zero.Unlike the
Atom.rezero
method, this method does not call the super classrezero
method.Parameters: epsilon (float) – smallest allowed absolute value of any x,y,z component.
-
todict
()[source] [edit on github][source]¶ Return
dict
of constructor parameters.