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.