sknano.core.atoms.MDAtoms

class sknano.core.atoms.MDAtoms(atoms=None, kNN=16, NNrc=2.0, **kwargs)

An Atoms sub-class for molecular dynamics trajectory analysis.

Sub-class of StructureAtoms class, and a container class for lists of MDAtom instances.

Parameters:

atoms : {None, sequence, MDAtoms}, optional

if not None, then a list of MDAtom instance objects or an existing MDAtoms instance object.

Attributes

CM	Alias for center_of_mass.
CN_counts	Alias for coordination_number_counts.
M	Total mass of Atoms.
NNrc	Nearest neighbor radius cutoff.
Natoms	Number of atoms in Atoms.
Ntypes	Number of unique types.
POAV1	List of POAVAtom POAV1 POAV1 attribute.
POAV2	List of POAVAtom POAV2 POAV2 attribute.
POAVR	List of POAVAtom POAVR POAVR attribute.
atom_ids	Alias for IDAtoms.ids.
atom_tree	KDTree of
atomtypes	Alias for types.
bounds	Bounds of Atoms.
center_of_mass	Center-of-Mass coordinates of Atoms.
centroid	Centroid of Atoms.
charges	Return array of ChargedAtom charges.
com	Alias for center_of_mass.
coordination_counts	Alias for coordination_number_counts.
coordination_number_counts	Coordination number counts.
coordination_numbers	ndarray of CNAtom.CNs.
coords	Alias for Atoms.r.
distances	Neighbor atoms distances.
dr	ndarray of Atom.dr displacement Vectors
elements	ndarray of Atom.elements in Atoms.
f	Alias for forces.
first_neighbors
fmtstr
forces	ndarray of ForceAtom forces.
fx	ndarray of Atoms \(f_x\) components.
fy	ndarray of Atoms \(f_y\) components.
fz	ndarray of Atoms \(f_z\) components.
i	Alias for images.
ids	Return array of IDAtom.ids.
images	ndarray of ImageAtom images.
inertia_tensor	Inertia tensor.
ix	ndarray of Atoms \(i_x\) values.
iy	ndarray of Atoms \(i_y\) values.
iz	ndarray of Atoms \(i_z\) values.
kNN	Number of nearest neighbors to return when querying the kd-tree.
kinetic_energies	ndarray of EnergyAtom.ke.
lattice
masses	ndarray of Atom.masss in Atoms.
mol_ids	Alias for IDAtoms.mols.
molecule_ids	Alias for IDAtoms.mols.
mols	Return array of IDAtom.mols.
nearest_neighbors	Return array of nearest-neighbor atoms for each KDTAtom.
neighbor_distances
neighbors	Return array of neighbor atoms.
pbc
potential_energies	ndarray of EnergyAtom.pe.
q	Return the total net charge of ChargedAtoms.
r	ndarray of Atom.r position Vectors
rs	ndarray of Atom.r position Vectors
second_neighbors
symbols	ndarray of Atom.symbols in Atoms.
third_neighbors
total_energies	ndarray of EnergyAtom.etotal.
typemap	dict of TypeAtom.types.
types	ndarray of TypeAtom.types.
v	Alias for velocities.
velocities	ndarray of VelocityAtom velocities.
volume	Volume of region containing atoms.
vx	ndarray of Atoms \(v_x\) components.
vy	ndarray of Atoms \(v_y\) components.
vz	ndarray of Atoms \(v_z\) components.
x	ndarray of Atoms \(x\) coordinates.
xs	ndarray of Atoms \(x\) coordinates.
y	ndarray of Atoms \(y\) coordinates.
ys	ndarray of Atoms \(y\) coordinates.
z	ndarray of Atoms \(z\) coordinates.
zs	ndarray of Atoms \(z\) coordinates.

Methods

add_atomtype(atom)	Alias for add_type.
add_atomtypes([atoms])	Alias for add_types.
add_type(atom)	Add atom type to typemap.
add_types([atoms])	Add atom type for each atom in atoms to TypeAtom.typemap dictionary.
append(atom)
assign_unique_ids([starting_id])	Assign unique IDAtom.id to each IDAtom in IDAtoms.
assign_unique_types([from_attr])	Assign unique TypeAtom.types to each TypeAtom in TypeAtoms from an existing unique atom attribute.
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.
compute_POAVs()	Compute POAV1, POAV2, POAVR.
compute_rdf()
copy()
count(item)
extend(other)
filter(condition[, invert])	Filter Atoms by condition.
filter_ids(atom_ids[, invert])	Filter Atoms by IDAtoms.ids in atom_ids.
filtered(condition[, invert])	Return new list of Atoms filtered by condition.
filtered_ids(atom_ids[, invert])	Return new Atoms filtered by IDAtoms.ids in atom_ids.
get_POAV_attr(POAV_class, attr)	Return list of POAVAtom POAV1 POAV2 or POAVR attribute.
get_atom(id)	Get IDAtom with Xatom.id == id.
get_atoms([asarray])	Return list of Atoms.
get_atomtypes([asdict])	Alias for get_types.
get_coords([asdict])	Return atom coords.
get_neighbors(n)
get_types([asdict])	Return list of TypeAtom TypeAtom.types.
getatomattr(attr)	Get ndarray of atom attributes attr.
index(item, *args)
insert(i, item)
mapatomattr([from_attr, to_attr, attrmap])	Set/update atom attribute from another atom attribute with dict.
neighbor_counts(r)
pop([i])
query_atom_tree([k, eps, p, rc])	Query atom tree for nearest neighbors distances and indices.
query_ball_point(pts, r[, p, eps])	Find all Atoms within distance r of point(s) pts.
remove(item)
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.
set_pbc([xperiodic, yperiodic, zperiodic])
sort([key, reverse])
todict()
translate(t[, fix_anchor_points])	Translate Atom vectors by Vector t.
unset_pbc()
update_attrs()	Update KDTAtoms attributes.
update_bonds()	Update KDTAtom.bonds.
update_neighbors([cutoffs])
wrap_coords([pbc])