MDMC.MD.ase package

Submodules

MDMC.MD.ase.convert module

Converts ASE Atoms objects into MDMC Molecules.

MDMC.MD.ase.convert.ASE_to_MDMC(atoms: Atoms) → List[Atom][source]

Convert an ASE Atoms object to a list of Atoms.

Parameters:: atoms (ase.Atoms) – an ASE Atoms object.
Returns:: a list of Atoms with bonds corresponding to the ASE Atoms object.
Return type:: List[Atom]

MDMC.MD.ase.convert.MDMC_to_ASE(structure: Structure | Universe | List[Atom], cell: ndarray | None = None) → Atoms[source]

Convert an MDMC Structure into an ase.Atoms object. Note that ASE infers bonds from the atoms’ covalent radius.

Parameters:

structure: Structure, Universe or List[Atom]: the MDMC object to convert.
cell: np.array, optional, default None: provides cell dimensions for the ASE Atoms object. If None, the default cell size (0,0,0) is used.

Returns:

ase.Atoms: an ASE Atoms object corresponding to the same structure.

Module contents

Contains the interface to the Atomic Simulation Environment (ASE). MDMC supports conversions between MDMC structures and the equivalent ASE objects.