eon.atoms

Atoms / structure helpers for the eOn Python server.

Storage and I/O :class:eon.structure.Structure (alias :class:Atoms) is the in-memory working type. On disk, structures are readcon.ConFrame values (see :func:eon.structure.Structure.from_conframe).

Geometry kernels PBC, neighbor lists (vesin), and process-atom selection live under :mod:eon.geometry. This module re-exports them for compatibility and keeps structure-matching / CNA helpers plus a radius/color overlay.

Module Contents

Functions

atomic_number	Z for a symbol. Integers pass through. Symbol lookup is readcon.
symbol_for_z	Chemical symbol for Z. Lookup is readcon; Z=0 is the unknown placeholder.
identical	True if two structures match when same-element atoms are interchangeable.
match
point_energy_match
points_energies_match
rot_match
rotm	Gives the matrix representing a rotation of theta radians about axis
cna	Common-neighbor labels for every atom in p.
not_HCP_or_FCC	Indices of atoms that are neither fcc nor hcp (CNA other).
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	Depth-first search for a complete atom mapping from a onto b.
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
CNA_FCC
CNA_HCP
CNA_OTHER
numElements
elements

API

eon.atoms.logger

‘getLogger(…)’

eon.atoms.atomic_number(symbol_or_z)

Z for a symbol. Integers pass through. Symbol lookup is readcon.

eon.atoms.symbol_for_z(z)

Chemical symbol for Z. Lookup is readcon; Z=0 is the unknown placeholder.

eon.atoms.identical(atoms1, atoms2, epsilon_r)

True if two structures match when same-element atoms are interchangeable.

Parameters

atoms1, atoms2 : Structure Configurations to compare (same box within 1e-4). epsilon_r : float Max allowed MIC displacement (Å) for a pair to count as the same site.

eon.atoms.match(a, b, eps_r, neighbor_cutoff, indistinguishable, check_rotation=False, use_identical=False)

eon.atoms.point_energy_match(file_a, energy_a, file_b, energy_b, eps_e, eps_r, neighbor_cutoff, check_rotation=False, use_identical=False)

eon.atoms.points_energies_match(file_a, energy_a, files_b, energies_b, eps_e, eps_r, neighbor_cutoff, check_rotation=False, use_identical=False)

eon.atoms.rot_match(a, b, eps_r)

eon.atoms.rotm(axis, theta)

Gives the matrix representing a rotation of theta radians about axis

eon.atoms.CNA_FCC

0

eon.atoms.CNA_HCP

1

eon.atoms.CNA_OTHER

2

eon.atoms.cna(p, cutoff)

Common-neighbor labels for every atom in p.

Labels match the C++ client (EpiCenters::cna): 0 fcc (421), 1 hcp (422), 2 other. Inspired by the CNA code provided by Asap (wiki.fysik.dtu.dk/asap).

eon.atoms.not_HCP_or_FCC(p, cutoff)

Indices of atoms that are neither fcc nor hcp (CNA other).

eon.atoms.cnat(p, cutoff)

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)

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)

Returns a list of indices for the atoms with cna = 0

eon.atoms.not_TCP_or_BCC(p, cutoff)

Returns a list of indices for the atoms with cna = 0

eon.atoms.get_mappings(a, b, eps_r, neighbor_cutoff, mappings=None)

Depth-first search for a complete atom mapping from a onto b.

Returns None if no mapping was found, or a dict mapping a indices to b indices. Mirror images still map; this does not test proper rotation.

eon.atoms.get_rotation_matrix(axis, theta)

eon.atoms.rotate(r, axis, center, angle)

eon.atoms.internal_motion(a, b)

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.numElements

‘len(…)’

eon.atoms.elements

‘_ElementStyle(…)’