ase_interface

Full Documentation for hippynn.interfaces.ase_interface package. Click here for a summary page.

For using hippynn with the Atomic Simulation Environment (ASE)

class AseDatabase(directory: str, name: str | List[str], inputs, targets, *args, quiet=False, allow_unfound=False, **kwargs)[source]

Bases: Database, Restartable

Database stored as ase database file(s) in a directory.

Parameters:

  • directory – directory path where the ase database(s) is stored

  • name – name or list of names for files for ase databases.

This function loads an ase database(s) ({name}.json/.db) OR ({{name}.extxyz,.xyz}) variable db_name including all inputs and targets.

filenames should end with .json, .db, .extxyz, and .xyz, etc; Anything parsable by ase.io.load

Other arguments: See Database.

See: https://databases.fysik.dtu.dk/ase/ase/db/db.html for documentation

on typical columns present in ase database

load_arrays(directory, filename, inputs, targets, quiet=False, allow_unfound=False)[source]

load arrays load ase database into hippynn database arrays

Parameters:

  • directory – directory where database is stored

  • filename – file or path to file from directory

  • inputs

  • targets

  • quiet

  • allow_unfound

Returns:

class HippynnCalculator(*args: Any, **kwargs: Any)[source]

Bases: Calculator

ASE calculator based on hippynn graphs. Uses ASE neighbor lists. Not suitable for domain decomposition.

calculate(atoms=None, properties=None, system_changes=True)[source]

Accepts ‘properties’ and ‘system changes’ but ignores them, purely for compatibility with ASE base calculator

calculation_required(atoms, properties=None, tol=1e-15)[source]

Returns true if: 1. A property in the list properties is not supported. 2. Atoms are different from stored atoms. This proceeds by short-circuit: * if this check is passed, compare using ase compare_atoms and tolerance tol. * slight difference from ASE implementation: if properties is a string then it is wrapped in a list.

get_charges(atoms, allow_calculation=True, **kwargs)
get_dipole(atoms, allow_calculation=True, **kwargs)
get_dipole_moment(atoms, allow_calculation=True, **kwargs)
get_energies(atoms, allow_calculation=True, **kwargs)
get_energy(atoms, allow_calculation=True, **kwargs)
get_forces(atoms, allow_calculation=True, **kwargs)
get_free_energy(atoms, allow_calculation=True, **kwargs)
get_magmom(atoms, allow_calculation=True, **kwargs)
get_magmoms(atoms, allow_calculation=True, **kwargs)
get_potential_energies(atoms, allow_calculation=True, **kwargs)
get_potential_energy(atoms, allow_calculation=True, **kwargs)
get_property(name, atoms, allow_calculation=True)[source]
get_stress(atoms, allow_calculation=True, **kwargs)
get_stresses(atoms, allow_calculation=True, **kwargs)
rebuild_neighbors()[source]
set_atoms(atoms)[source]
to(*args, **kwargs)[source]
calculator_from_model(model, **kwargs)[source]

Attempt to find the energy and charge nodes automatically.

Parameters:

Note

If your model has an energy node, but that is not the full energy for simulation, don’t use this function. Similarly for charge.

Submodules