# pymatgen.analysis.transition_state module¶

Some reimplementation of Henkelman’s Transition State Analysis utilities, which are originally in Perl. Additional features beyond those offered by Henkelman’s utilities will be added.

This allows the usage and customization in Python.

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.

combine_neb_plots(neb_analyses, arranged_neb_analyses=False, reverse_plot=False)[source]

neb_analyses: a list of NEBAnalysis objects

arranged_neb_analyses: The code connects two end points with the smallest-energy difference. If all end points have very close energies, it’s likely to result in an inaccurate connection. Manually arrange neb_analyses if the combined plot is not as expected compared with all individual plots. E.g., if there are two NEBAnalysis objects to combine, arrange in such a way that the end-point energy of the first NEBAnalysis object is the start-point energy of the second NEBAnalysis object. Note that the barrier labeled in y-axis in the combined plot might be different from that in the individual plot due to the reference energy used. reverse_plot: reverse the plot or percolation direction. return: a NEBAnalysis object