matscipy.hydrogenate
Functions
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Hydrogenate a slab of material at its periodic boundary conditions. |
- matscipy.hydrogenate.hydrogenate(a, cutoff, bond_length, b=None, mask=[True, True, True], exclude=None, vacuum=None)
Hydrogenate a slab of material at its periodic boundary conditions. Boundary conditions are turned into nonperiodic.
- Parameters:
a (ase.Atoms) – Atomic configuration.
cutoff (float) – Cutoff for neighbor counting.
bond_length (float) – X-H bond length for hydrogenation.
b (ase.Atoms, optional) – If present, this is the configuration to hydrogenate. Number of atoms must be identical to a object. All bonds present in a but not present in b will be hydrogenated in b.
mask (list of bool) – Cartesian directions which to hydrogenate, only if b argument is not given.
exclude (array_like) – Boolean array masking atoms to be excluded from hydrogenation.
vacuum (float, optional) – Add this much vacuum after hydrogenation.
- Returns:
a – Atomic configuration of the hydrogenated slab.
- Return type:
ase.Atoms