matscipy.calculators.mcfm.qm_cluster_tools.base_qm_cluster_tool

Classes

BaseQMClusterTool(mediator)

Class that hold all the functions common to qm clustering objects
class matscipy.calculators.mcfm.qm_cluster_tools.base_qm_cluster_tool.BaseQMClusterTool(mediator)

Bases: object

Class that hold all the functions common to qm clustering objects

Methods

find_neighbours(atoms, index)

Find the neighbours of atom i using self.neighbour_list returns a list of [heavy_neighbours, hydrogen_neighbours]

hydrogenate_cluster(atoms, cluster)

Add neigoburing hydrogens to a cluster composed of heavy ions The input should be a set representing heavy ions in a cluster This functions operates on sets
__init__(mediator)

Class that hold all the functions common to qm clustering objects

Parameters:

mediator (matscipy.calculators.mcfm.QMCluster) – class responsible for managing the QM clusters in the simulation

find_neighbours(atoms, index)

Find the neighbours of atom i using self.neighbour_list returns a list of [heavy_neighbours, hydrogen_neighbours]

Parameters:

  • atoms (ase.Atoms object) – structure in which it is necessary to find the neighbours

  • index (int) – atomic index

Returns:

  • list – non-hydrogen neighbours

  • list – hydrogen neighbours

hydrogenate_cluster(atoms, cluster)

Add neigoburing hydrogens to a cluster composed of heavy ions The input should be a set representing heavy ions in a cluster This functions operates on sets

Parameters:

  • atoms (ase.Atoms object) – structure in which it is necessary to find the neighbours

  • cluster (ase.Atoms object) – sub-structure of the larger struct that needs its dangling bonds hydrogenated

Returns:

The original cluster but now hydrogenated

Return type:

ase.Atoms