ase_database module

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

Dataset stored as ase database file (ideally either .json or .db, or in .xyz, .extxyz formats)

See: https://databases.fysik.dtu.dk/ase/ase/db/db.html for documentation on typical columns present in ase database

Typically used column names in ase db/xyz format:

positions : x,y,z cartesian positions (Angstrom) forces : x,y,z carteisian forces (ev/Angstrom) energy : energy (eV) energy_per_atom : energy per atom (eV/atom) cell : x,y,z of cell (3x3) (Angstrom) charges : atom-specific charges stress: (6,) atomic stresses initial_charges : atom-specific initial charges inital_magmoms :atom-specific initial magnetic moments numbers : atom Zs (integer) pbc : periodic boundary conditions (bool) ctime : computer time (float) mtime : time (float) dipole : molecular dipole (3) vector

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

Bases: AseMethods, Database, Restartable

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

class AseDatabaseIterable(iterable, inputs, targets, *args, quiet=False, allow_unfound=False, **kwargs)

Bases: AseMethods, Database

load_arrays(iterable, inputs, targets, quiet=False, allow_unfound=False)

class AseMethods

Bases: object

read_from_iterable(iterable, inputs, targets, quiet=False, allow_unfound=False)