narupa.ase.converter module

Module containing methods for converting between ASE simulations consisting of Atoms and the Narupa FrameData object for transmission to Narupa clients.

narupa.ase.converter.add_ase_box_vectors_to_frame_data(data: narupa.trajectory.frame_data.FrameData, ase_atoms: ase.atoms.Atoms)

Adds the periodic box vectors from the given ASE Atoms object to the given FrameData.

Parameters:
  • data – FrameData upon which to add periodic box vectors.
  • ase_atoms – Atoms from which to extract periodic box vectors.
narupa.ase.converter.add_ase_positions_to_frame_data(data: narupa.trajectory.frame_data.FrameData, positions: numpy.array)

Adds ASE positions to the frame data, converting to nanometers.

Parameters:
  • data – FrameData to add atom positions to.
  • positions – Array of atomic positions, in angstroms.
narupa.ase.converter.add_ase_state_to_frame_data(frame_data: narupa.trajectory.frame_data.FrameData, ase_atoms: ase.atoms.Atoms)

Adds simulation state information to the frame, consisting of the potential energy and kinetic energy.

Parameters:
  • frame_data – Frame data to add ASE state information to.
  • ase_atoms – The ASE atoms from which to extract state information.
narupa.ase.converter.add_ase_topology_to_frame_data(frame_data: narupa.trajectory.frame_data.FrameData, ase_atoms: ase.atoms.Atoms, generate_bonds=True)

Generates a topology for the current state of the atoms and adds it to the frame.

Since ASE atoms have no concept of bonds, they are generated using distance criteria.

Parameters:
  • frame_data – Frame data to add topology information to.
  • ase_atoms – ASE atoms to extract topology information from.
narupa.ase.converter.add_frame_data_positions_to_ase(frame_data, ase_atoms)

Adds frame data particle positions to ASE atoms, converting to angstroms.

Parameters:
  • frame_data – FrameData from which to extract positions.
  • ase_atoms – ASE Atoms to add particle positions to.
narupa.ase.converter.add_frame_data_topology_to_ase(frame_data: narupa.trajectory.frame_data.FrameData, atoms: ase.atoms.Atoms)

Adds frame data topology information to ASE Atoms.

Since ASE Atoms do not have a concept of bonds, this just adds particle elements.

Parameters:
  • frame_data – FrameData from which to extract topology.
  • atoms – ASE Atoms to add element data to.
narupa.ase.converter.ase_to_frame_data(ase_atoms: ase.atoms.Atoms, positions: bool = True, topology: bool = True, state: bool = True, box_vectors: bool = True, generate_bonds: bool = True) → narupa.trajectory.frame_data.FrameData

Constructs a Narupa frame from the state of the atoms in an ASE simulation.

Parameters:
  • ase_atoms – The ASE atoms object representing the state of the simulation to send.
  • positions – Whether to add positions to the frame.
  • topology – Whether to generate the current state of the topology and add it to the frame.
  • state – Whether to add additional state information such as energies.
  • box_vectors – Whether to add the box vectors to the frame data.
  • generate_bonds – Whether to generate bonds for the topology.
Returns:

Narupa frame.
Raises:

AttributeError Raised if state is True, and ase_atoms has no calculator attached.

 
>>> atoms = Atoms('CO', positions=[(0, 0, 0), (0, 0, 1.1)], cell=[2, 2, 2])
>>> frame = ase_to_frame_data(atoms, state=False)
>>> frame.particle_count
2
>>> frame.bonds
[[0, 1]]
>>> frame.particle_elements
[6, 8]
narupa.ase.converter.frame_data_to_ase(frame_data: narupa.trajectory.frame_data.FrameData, positions: bool = True, topology: bool = True, ase_atoms: Optional[ase.atoms.Atoms] = None) → ase.atoms.Atoms

Constructs an ASE Atoms object from a Narupa FrameData.

Parameters:
  • frame_data – The Narupa FrameData.
  • positions – Whether to add positions to the ASE atoms.
  • topology – Whether to add topology information within the frame data to ASE.
  • ase_atoms – Optional ASE Atoms object, which will have its positions replaced. If the flag topology is set, then a new object will still be constructed.
Returns:

ASE Atoms updated or created with the data contained in the Narupa frame.

 
>>> frame = FrameData()
>>> frame.particle_elements = [6, 8]
>>> frame.particle_positions = [[0,0,0], [0,0, 0.11]]
>>> atoms = frame_data_to_ase(frame)
>>> atoms.symbols
Symbols('CO')
narupa.ase.converter.generate_bonds_from_ase(atoms: ase.atoms.Atoms)

Generates bonds for the given configuration of ASE atoms using a distance criterion.

A bond is placed between two atoms if the distance between them is less than 0.6 times the VDW radii of the atoms.

Parameters:atoms – ASE atoms to generate bonds for.
Returns:A list of pairs of atom indexes representing bonds.

The following example produces a bond between the two atoms in a carbon monoxide molecule:

>>> co = Atoms('CO', positions=[(0, 0, 0), (0, 0, 1.1)], cell=[2, 2, 2])
>>> generate_bonds(co)
[[0, 1]]
narupa.ase.converter.get_radius_of_element(symbol: str, default=1.0)

Gets the radius of an atom in Angstroms.

Parameters:
  • symbol – The chemical symbol representing the element.
  • default – Default radius to use if the radius for the given chemical symbol is not known.
Returns:

The VDW radius of the atom in angstroms.