pymatgen.analysis.transition_state module

class NEBAnalysis(r, energies, forces, structures, spline_options=None)[source]

Bases: monty.json.MSONable

An NEBAnalysis class.

Initializes an NEBAnalysis from the cumulative root mean squared distances between structures, the energies, the forces, the structures and the interpolation_order for the analysis.

Parameters:
  • r – Root mean square distances between structures
  • energies – Energies of each structure along reaction coordinate
  • forces – Tangent forces along the reaction coordinate.
  • structures ([Structure]) – List of Structures along reaction coordinate.
  • spline_options (dict) – Options for cubic spline. For example, {“saddle_point”: “zero_slope”} forces the slope at the saddle to be zero.
as_dict()[source]

Dict representation of NEBAnalysis.

Returns:JSON serializable dict representation.
classmethod from_dir(root_dir, relaxation_dirs=None, **kwargs)[source]

Initializes a NEBAnalysis object from a directory of a NEB run. Note that OUTCARs must be present in all image directories. For the terminal OUTCARs from relaxation calculations, you can specify the locations using relaxation_dir. If these are not specified, the code will attempt to look for the OUTCARs in 00 and 0n directories, followed by subdirs “start”, “end” or “initial”, “final” in the root_dir. These are just some typical conventions used preferentially in Shyue Ping’s MAVRL research group. For the non-terminal points, the CONTCAR is read to obtain structures. For terminal points, the POSCAR is used. The image directories are assumed to be the only directories that can be resolved to integers. E.g., “00”, “01”, “02”, “03”, “04”, “05”, “06”. The minimum sub-directory structure that can be parsed is of the following form ( a 5-image example is shown):

00: - POSCAR - OUTCAR 01, 02, 03, 04, 05: - CONTCAR - OUTCAR 06: - POSCAR - OUTCAR

Parameters:
  • root_dir (str) – Path to the root directory of the NEB calculation.
  • relaxation_dirs (tuple) – This specifies the starting and ending relaxation directories from which the OUTCARs are read for the terminal points for the energies.
Returns:

NEBAnalysis object.

classmethod from_outcars(outcars, structures, **kwargs)[source]

Initializes an NEBAnalysis from Outcar and Structure objects. Use the static constructors, e.g., from_dir instead if you prefer to have these automatically generated from a directory of NEB calculations.

Parameters:
  • outcars ([Outcar]) – List of Outcar objects. Note that these have to be ordered from start to end along reaction coordinates.
  • structures ([Structure]) – List of Structures along reaction coordinate. Must be same length as outcar.
  • interpolation_order (int) – Order of polynomial to use to interpolate between images. Same format as order parameter in scipy.interplotate.PiecewisePolynomial.
get_extrema(normalize_rxn_coordinate=True)[source]

Returns the positions of the extrema along the MEP. Both local minimums and maximums are returned.

Parameters:normalize_rxn_coordinate (bool) – Whether to normalize the reaction coordinate to between 0 and 1. Defaults to True.
Returns:(min_extrema, max_extrema), where the extrema are given as [(x1, y1), (x2, y2), ...].
get_plot(normalize_rxn_coordinate=True, label_barrier=True)[source]

Returns the NEB plot. Uses Henkelman’s approach of spline fitting each section of the reaction path based on tangent force and energies.

Parameters:
  • normalize_rxn_coordinate (bool) – Whether to normalize the reaction coordinate to between 0 and 1. Defaults to True.
  • label_barrier (bool) – Whether to label the maximum barrier.
Returns:

matplotlib.pyplot object.

setup_spline(spline_options=None)[source]

Setup of the options for the spline interpolation

Parameters:spline_options (dict) – Options for cubic spline. For example, {“saddle_point”: “zero_slope”} forces the slope at the saddle to be zero.