BasisAtoms

class sknano.core.atoms.BasisAtoms(*args, xperiodic=False, yperiodic=False, zperiodic=False, **kwargs)

Bases: sknano.core.atoms.mixins.AtomsTransformationsMixin, sknano.core.atoms.mixins.BoundingRegionsMixin, sknano.core.atoms.lattice_atoms.LatticeAtoms, sknano.core.atoms.xyz_atoms.XYZAtoms

An Atoms sub-class for crystal structure basis atoms.

Sub-class of Atoms class, and a container class for lists of BasisAtom instances.

Parameters:atoms ({None, sequence, BasisAtoms}, optional) – if not None, then a list of BasisAtom instance objects or an existing BasisAtoms instance object.

Attributes

CM	Alias for center_of_mass.
M	Total mass of Atoms.
Natoms	Number of atoms in Atoms.
bounding_box	Axis-aligned bounding box of Atoms.
bounding_region	Bounding Geometric3DRegion.
bounding_sphere	Bounding Sphere of Atoms.
bounds	Alias for bounding_region.
cell	Alias for LatticeAtoms.cell_matrix.
cell_matrix	Return the Crystal3DLattice.cell_matrix.
center_of_mass	Center-of-Mass coordinates of Atoms.
centroid	Centroid of Atoms.
com	Alias for center_of_mass.
coordinates_bounding_box	Bounding box of atom coordinates.
coords	Alias for Atoms.r.
dr	Vectors of Atom.dr displacement Vectors
elements	ndarray of Atom.elements.
fmtstr	Format string.
inertia_tensor	Return inertia tensor about the origin.
lattice	Return the LatticeAtom.lattice of the first atom in self.
lattice_region	lattice region.
masses	ndarray of Atom.masss.
moment_of_inertia	Alias for inertia_tensor.
pbc	Return boolean array of periodic boundaries set along x,y,z axes.
positions	Alias for Atoms.r.
principal_axes	Return principal axes of rotation computed from the inertia tensor.
principal_moments_of_inertia	Return principal moments of inertia.
r	Vectors of Atom.r position Vectors
radius_of_gyration	Return radius of gyration.
rs	Vectors of LatticeAtom.rs Vectors
symbols	ndarray of Atom.symbols.
volume	Volume of region containing atoms.
x	ndarray of XYZAtom.x coordinates.
xperiodic	Return True if periodic along the x axis.
xs	ndarray of LatticeAtom.xs values
y	ndarray of XYZAtom.y coordinates.
yperiodic	Return True if periodic along the y axis.
ys	ndarray of LatticeAtom.ys values
z	ndarray of XYZAtom.z coordinates.
zperiodic	Return True if periodic along the z axis.
zs	ndarray of LatticeAtom.zs values

Methods

align_principal_axis(index, vector)	Align principal_axes`[`index] along vector.
append(atom)
center_CM([axis])	Alias for center_center_of_mass.
center_center_of_mass([axis])	Center atoms on center-of-mass coordinates.
center_centroid()	Center centroid on origin.
center_com([axis])	Alias for center_center_of_mass.
clear()
clip_bounds(region[, center_before_clipping])	Remove atoms outside the given region.
copy()
count(item)
extend(other)
filter(condition[, invert])	Filter Atoms by condition.
filtered(condition[, invert])	Return new list of Atoms filtered by condition.
get_atoms([asarray, aslist])	Return Atoms either as list (default) or numpy array or self.
get_coords([asdict])	Return atom coords.
getattr(attr[, default, recursive])	Get ndarray of atom attributes attr.
index(item, *args)
insert(i, atom)
mapatomattr([from_attr, to_attr, attrmap])	Set/update atom attribute from another atom attribute with dict.
pop([i])
remove(item)
reset_attrs(**kwargs)	Call corresponding reset_attrs method on each atom
reverse()
rezero([epsilon])	Set values with absolute value less than epsilon to zero.
rezero_coords([epsilon])	Alias for Atoms.rezero_xyz.
rezero_xyz([epsilon])	Rezero position vector components with absolute value less than epsilon.
rotate(**kwargs)	Rotate Atom vectors.
select([selstr, selstrlist, verbose])	Return Atom or Atoms from selection command.
set_pbc(dims)	Set periodic boundaries along dims.
sort([key, reverse])
todict()	Return dict of constructor parameters.
translate(t[, fix_anchor_points, cartesian])	Translate Atom vectors by Vector t.
unset_pbc()	Turn of PBCs along all dimensions.
update_attrs(**kwargs)	Call update_attrs method on each atom.
within_region(region)	Returns new Atoms object containing atoms within region.
wrap_coords([pbc])	Wrap coordinates into lattice.