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: 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)

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: