pymatgen.analysis.diffusion.neb.io module

Generate input fields for NEB calculations.

class MVLCINEBEndPointSet(structure, **kwargs)[source]

Bases: MITRelaxSet

Class for writing NEB end points relaxation inputs.

Parameters:

  • structure – Structure

  • **kwargs – Keyword args supported by VaspInputSets.

class MVLCINEBSet(structures, **kwargs)[source]

Bases: MITNEBSet

MAVRL-tested settings for CI-NEB calculations. Note that these parameters requires the VTST modification of VASP from the Henkelman group. See http://theory.cm.utexas.edu/vtsttools/.

Parameters:

  • structures – Input structures.

  • **kwargs – Keyword args supported by VaspInputSets.

get_endpoint_dist(ep_0, ep_1)[source]

Calculate a list of site distances between two endpoints, assuming periodic boundary conditions.

Parameters:

  • ep_0 (Structure) – the first endpoint structure.

  • ep_1 (Structure) – the second endpoint structure.

Returns:

a list of distances between two structures.

Return type:

dist (list)

get_endpoints_from_index(structure, site_indices)[source]

This class reads in one perfect structure and the two endpoint structures are generated using site_indices.

Parameters:

  • structure (Structure) – A perfect structure.

  • site_indices (list of int) – a two-element list indicating site indices.

Returns:

a two-element list of two endpoints

Structure object.

Return type:

endpoints (list of Structure)