ase/structure format

ase/structure format#

Class: ASEStructureFormat

Format for the Atomic Simulation Environment (ase).

ASE supports parsing a few dozen of data formats. As described in i the documentation, many of these formats can be determined automatically. Use the ase_fmt keyword argument to supply the format if automatic detection fails.

Conversions#

Convert from this format to System#

dpdata.System(atoms: 'ase.Atoms', fmt: Literal['ase/structure'] = None) → dpdata.system.System
dpdata.System.from_ase_structure(atoms: 'ase.Atoms') → dpdata.system.System

Convert ase.Atoms to a System.

Parameters:
atomsase.Atoms

an ASE Atoms, containing a structure

Returns:
System

converted system

Convert from System to this format#

dpdata.System.to(fmt: Literal['ase/structure']) → 'list[ase.Atoms]'
dpdata.System.to_ase_structure() → 'list[ase.Atoms]'

Convert System to ASE Atom obj.

Convert from LabeledSystem to this format#

dpdata.LabeledSystem.to(fmt: Literal['ase/structure']) → 'list[ase.Atoms]'
dpdata.LabeledSystem.to_ase_structure() → 'list[ase.Atoms]'

Convert System to ASE Atoms object.

Convert from this format to LabeledSystem#

dpdata.LabeledSystem(atoms: 'ase.Atoms', fmt: Literal['ase/structure'] = None) → dpdata.system.LabeledSystem
dpdata.LabeledSystem.from_ase_structure(atoms: 'ase.Atoms') → dpdata.system.LabeledSystem

Convert ase.Atoms to a LabeledSystem. Energies and forces are calculated by the calculator.

Parameters:
atomsase.Atoms

an ASE Atoms, containing a structure

Returns:
LabeledSystem

converted system

Raises:
RuntimeError

ASE will raise RuntimeError if the atoms does not have a calculator

Convert from this format to MultiSystems#

dpdata.MultiSystems.from_ase_structure(file_name: 'str', begin: 'int | None' = None, end: 'int | None' = None, step: 'int | None' = None, ase_fmt: 'str | None' = None) → dpdata.system.MultiSystems

Convert a ASE supported file to ASE Atoms.

It will finally be converted to MultiSystems.

Parameters:
file_namestr

path to file

beginint, optional

begin frame index

endint, optional

end frame index

stepint, optional

frame index step

ase_fmtstr, optional

ASE format. See the ASE documentation about supported formats

Returns:
MultiSystems

converted system