Classify ASE Atoms#

Problem#

You have an ASE Atoms and want CHILL+ labels or cage flags on the same configuration, then an Atoms back with those arrays.

Install the extra#

pip install 'pydseamslib[ase]'

Without it, from_ase / to_ase raise ImportError and name that command.

Classify ASE Atoms#

import ase.io
import pydseams as ds

atoms = ase.io.read("water.lammpstrj", format="lammps-dump-text")
frame = ds.from_ase(atoms)
print(frame.chill_plus())
labelled = frame.to_ase()

from_ase is Frame.from_ase. The cell must be nonsingular and periodic in all three directions. Orthorhombic and general triclinic cells are supported. from_ase keeps oxygen by default (select="O").

Select and bonding#

Pass a symbol, an atomic number, None (every atom), or a sequence:

#skip_lint_start

frame = ds.from_ase(atoms, select="O")
frame = ds.from_ase(atoms, select=8)
frame = ds.from_ase(atoms, select=None)
frame = ds.from_ase(atoms, select=("O", "Na", "Cl"))

#skip_lint_end

A sequence keeps every listed species in the cloud and analyses the first. Ions stay in the cloud for pydseams.features.ion_environment.

bonded="auto" uses hydrogen bonds only when the Atoms include H and the selected analysis cloud excludes H. The default oxygen selection on molecular water therefore uses hydrogen bonds, while select=None uses the cutoff neighbour list. Single-site models (mW) also use the cutoff neighbour list:

frame = ds.from_ase(atoms, select="O", bonded="cutoff")

bonded is "auto", "hbond", or "cutoff". Explicit bonded="hbond" requires a heavy-atom selection such as select="O". For that selection, hydrogens stay in a side cloud so the analysed species remain the CHILL / ring particles.

If atoms.arrays["mol-id"] exists, its molecule IDs associate each hydrogen with its selected donor atom. Otherwise, from_ase assigns each hydrogen to the nearest selected atom using ASE’s periodic minimum-image distance. Ordinary O H H water ordering does not need extra metadata.

Labels on the way back#

to_ase rebuilds an Atoms with the analysed positions and the imported cell orientation and displacement (pbc=True). General cells are represented internally in LAMMPS restricted-triclinic form. After chill_plus / chill, atoms.arrays["ice_type"] holds the per-atom names. After cages(), atoms.arrays["hc"] and atoms.arrays["ddc"] hold the last CageScore. atoms.info["dseams_n_atoms"] is the analysed particle count.

A frame loaded from a LAMMPS dump (no ASE symbols) uses O as the fallback species.

Classify ASE Atoms#

Problem#

Install the extra#

Classify ASE Atoms#

Select and bonding#

Labels on the way back#

See also#