ASESystem

class narupatools.ase.system.ASESystem(atoms: ase.atoms.Atoms, *, universe: Optional[MDAnalysis.core.universe.Universe] = None)

Wrapper around an ASE Atoms object so it is exposed consistently.

Inheritance

Methods

__init__	Create a wrapper around the given ASE Atoms object.
create	Create a an ASE system which can be broadcast through a session.
get_frame	Create a FrameData representation, with the given fields present if available.

__init__(atoms: ase.atoms.Atoms, *, universe: Optional[MDAnalysis.core.universe.Universe] = None)

Create a wrapper around the given ASE Atoms object.

Parameters

• atoms – ASE Atoms to wrap.

• universe – Optional MDAnalysis universe containing additional information.

static create(atoms: ase.atoms.Atoms, *, universe: Optional[MDAnalysis.core.universe.Universe] = None) → narupatools.ase.system.ASESystem

Create a an ASE system which can be broadcast through a session.

If the Atoms object does not have a calculator, a null calculator will be added.

Parameters

• atoms – ASE atoms object.

• universe – Optional MDAnalysis universe with additional system information.

Returns

Representation of the system which can be broadcast through a session.

get_frame(fields: infinite_sets.infinite_sets.InfiniteSet[str]) → narupa.trajectory.frame_data.FrameData

Create a FrameData representation, with the given fields present if available.

Parameters

fields – Collection of fields that should be added to FrameData if available.

Attributes

atoms

Wrapped ASE atoms object represented by this system.

atoms

Wrapped ASE atoms object represented by this system.