eon.atoms

`eon.atoms`#

The atoms module.

Module Contents#

Classes#

Atoms

The Atoms class.

Functions#

`pbc`	Applies periodic boundary conditions. Parameters: r: the vector the boundary conditions are applied to box: the box that defines the boundary conditions ibox: the inverse of the box. This will be calcluated if not provided.
`per_atom_norm`	Returns a length N numpy array containing per atom distance v: an Nx3 numpy array box: box matrix that defines the boundary conditions ibox: the inverse of the box. will be calculated if not provided
`per_atom_norm_gen`	Returns a generator which yields the distance between pairs of atoms v: an Nx3 numpy array box: box matrix that defines the boundary conditions ibox: the inverse of the box. will be calculated if not provided
`get_process_atoms`	Given the reactant and product configurations of a process, return the atoms that move significantly and their neighbors along the trajectory.
`identical`	Determines whether two structures are identical if atoms of the same element are considered indistinguishable. atoms1: first atoms object for comparison atoms2: second atoms object for comparison epsilon_r: distance (in angstroms) that two atoms must be seperated by in order to be considered different
`brute_neighbor_list`
`sweep_and_prune`	Returns a list of nearest neighbors within cutoff for each atom. Parameters: p_in: Atoms object cutoff: the radius within which two atoms are considered to intersect. strict: perform an actual distance check if True bc: include neighbors across pbc’s
`neighbor_list`
`neighbor_list_vectors`	Points from center to neighbor
`coordination_numbers`	Returns a list of coordination numbers for each atom in p
`least_coordinated`	Returns a list of atom indices in p with the lowest coordination numbers for unfrozen atoms
`match`
`point_energy_match`
`points_energies_match`
`rot_match`
`rotm`	Gives the matrix representing a rotation of theta radians about axis
`cna`	Returns a list of cna numbers for all atoms in p Inspired by the CNA code provided by Asap (wiki.fysik.dtu.dk/asap)
`not_HCP_or_FCC`	Returns a list of indices for the atoms with cna = 0
`cnat`	Returns a list of cna numbers for all atoms in p Inspired by the CNA code provided by Asap (wiki.fysik.dtu.dk/asap)
`cnar`	Returns a list of cna numbers for all atoms in p Inspired by the CNA code provided by Asap (wiki.fysik.dtu.dk/asap)
`not_TCP`	Returns a list of indices for the atoms with cna = 0
`not_TCP_or_BCC`	Returns a list of indices for the atoms with cna = 0
`get_mappings`	A recursive depth-first search for a complete set of mappings from atoms in configuration a to atoms in configuration b. Do not use the mappings argument, this is only used internally for recursion.
`get_rotation_matrix`
`rotate`
`internal_motion`	Takes two atoms objects and returns the motion from a to b that is entirely internal - no rotation or translation, in the form of a new atoms object.

Data#

`logger`
`elements`
`numElements`

API#

eon.atoms.logger#: ‘getLogger(…)’

class eon.atoms.Atoms(n_atoms)[source]#

The Atoms class.

Initialization

copy()[source]#

free_r()[source]#

append(r, free, name, mass)[source]#

eon.atoms.pbc(r, box, ibox=None)[source]#: Applies periodic boundary conditions. Parameters: r: the vector the boundary conditions are applied to box: the box that defines the boundary conditions ibox: the inverse of the box. This will be calcluated if not provided.

eon.atoms.per_atom_norm(v, box, ibox=None)[source]#: Returns a length N numpy array containing per atom distance v: an Nx3 numpy array box: box matrix that defines the boundary conditions ibox: the inverse of the box. will be calculated if not provided

eon.atoms.per_atom_norm_gen(v, box, ibox=None)[source]#: Returns a generator which yields the distance between pairs of atoms v: an Nx3 numpy array box: box matrix that defines the boundary conditions ibox: the inverse of the box. will be calculated if not provided

eon.atoms.get_process_atoms(r, p, epsilon_r=0.2, nshells=1)[source]#: Given the reactant and product configurations of a process, return the atoms that move significantly and their neighbors along the trajectory.

eon.atoms.identical(atoms1, atoms2)[source]#: Determines whether two structures are identical if atoms of the same element are considered indistinguishable. atoms1: first atoms object for comparison atoms2: second atoms object for comparison epsilon_r: distance (in angstroms) that two atoms must be seperated by in order to be considered different

eon.atoms.brute_neighbor_list(p, cutoff)[source]#

eon.atoms.sweep_and_prune(p_in, cutoff, strict=True, bc=True)[source]#: Returns a list of nearest neighbors within cutoff for each atom. Parameters: p_in: Atoms object cutoff: the radius within which two atoms are considered to intersect. strict: perform an actual distance check if True bc: include neighbors across pbc’s

eon.atoms.neighbor_list(p, cutoff, brute=False)[source]#

eon.atoms.neighbor_list_vectors(p, cutoff, brute=False)[source]#: Points from center to neighbor

eon.atoms.coordination_numbers(p, cutoff, brute=False)[source]#: Returns a list of coordination numbers for each atom in p

eon.atoms.least_coordinated(p, cutoff, brute=False)[source]#: Returns a list of atom indices in p with the lowest coordination numbers for unfrozen atoms

eon.atoms.match(a, b, eps_r, neighbor_cutoff, indistinguishable)[source]#

eon.atoms.point_energy_match(file_a, energy_a, file_b, energy_b)[source]#

eon.atoms.points_energies_match(file_a, energy_a, files_b, energies_b)[source]#

eon.atoms.rot_match(a, b)[source]#

eon.atoms.rotm(axis, theta)[source]#: Gives the matrix representing a rotation of theta radians about axis

eon.atoms.cna(p, cutoff, brute=False)[source]#: Returns a list of cna numbers for all atoms in p Inspired by the CNA code provided by Asap (wiki.fysik.dtu.dk/asap)

eon.atoms.not_HCP_or_FCC(p, cutoff, brute=False)[source]#: Returns a list of indices for the atoms with cna = 0

eon.atoms.cnat(p, cutoff, brute=False)[source]#: Returns a list of cna numbers for all atoms in p Inspired by the CNA code provided by Asap (wiki.fysik.dtu.dk/asap)

eon.atoms.cnar(p, cutoff, brute=False)[source]#: Returns a list of cna numbers for all atoms in p Inspired by the CNA code provided by Asap (wiki.fysik.dtu.dk/asap)

eon.atoms.not_TCP(p, cutoff, brute=False)[source]#: Returns a list of indices for the atoms with cna = 0

eon.atoms.not_TCP_or_BCC(p, cutoff, brute=False)[source]#: Returns a list of indices for the atoms with cna = 0

eon.atoms.get_mappings(a, b, eps_r, neighbor_cutoff, mappings=None)[source]#

A recursive depth-first search for a complete set of mappings from atoms in configuration a to atoms in configuration b. Do not use the mappings argument, this is only used internally for recursion.

Returns None if no mapping was found, or a dictionary mapping atom indices a to atom indices b.

Note: If a and b are mirror images, this function will still return a mapping from a to b, even though it may not be possible to align them through translation and rotation.

eon.atoms.get_rotation_matrix(axis, theta)[source]#

eon.atoms.rotate(r, axis, center, angle)[source]#

eon.atoms.internal_motion(a, b)[source]#: Takes two atoms objects and returns the motion from a to b that is entirely internal - no rotation or translation, in the form of a new atoms object.

eon.atoms.elements#: None

eon.atoms.numElements#: 119