Source code for pymatgen.analysis.transition_state

# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.

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.

import os
import glob

import numpy as np
from monty.json import jsanitize
from monty.json import MSONable

from pymatgen.util.plotting import pretty_plot
from import Poscar, Outcar
from pymatgen.analysis.structure_matcher import StructureMatcher
scipy_old_piecewisepolynomial = True
    from scipy.interpolate import PiecewisePolynomial
except ImportError:
    from scipy.interpolate import CubicSpline

    scipy_old_piecewisepolynomial = False

__author__ = 'Shyue Ping Ong'
__copyright__ = 'Copyright 2013, The Materials Virtual Lab'
__version__ = '0.1'
__maintainer__ = 'Shyue Ping Ong'
__email__ = ''
__date__ = '6/1/15'

[docs]class NEBAnalysis(MSONable): """ An NEBAnalysis class. """ def __init__(self, r, energies, forces, structures, spline_options=None): """ 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. Args: 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. """ self.r = np.array(r) self.energies = np.array(energies) self.forces = np.array(forces) self.structures = structures self.spline_options = spline_options if spline_options is not None \ else {} # We do a piecewise interpolation between the points. Each spline ( # cubic by default) is constrained by the boundary conditions of the # energies and the tangent force, i.e., the derivative of # the energy at each pair of points. self.setup_spline(spline_options=self.spline_options)
[docs] def setup_spline(self, spline_options=None): """ Setup of the options for the spline interpolation Args: spline_options (dict): Options for cubic spline. For example, {"saddle_point": "zero_slope"} forces the slope at the saddle to be zero. """ self.spline_options = spline_options relative_energies = self.energies - self.energies[0] if scipy_old_piecewisepolynomial: if self.spline_options: raise RuntimeError('Option for saddle point not available with' 'old scipy implementation') self.spline = PiecewisePolynomial( self.r, np.array([relative_energies, -self.forces]).T, orders=3) else: # New scipy implementation for scipy > 0.18.0 if self.spline_options.get('saddle_point', '') == 'zero_slope': imax = np.argmax(relative_energies) self.spline = CubicSpline(x=self.r[:imax + 1], y=relative_energies[:imax + 1], bc_type=((1, 0.0), (1, 0.0))) cspline2 = CubicSpline(x=self.r[imax:], y=relative_energies[imax:], bc_type=((1, 0.0), (1, 0.0))) self.spline.extend(c=cspline2.c, x=cspline2.x[1:]) else: self.spline = CubicSpline(x=self.r, y=relative_energies, bc_type=((1, 0.0), (1, 0.0)))
[docs] @classmethod def from_outcars(cls, outcars, structures, **kwargs): """ Initializes an NEBAnalysis from Outcar and Structure objects. Use the static constructors, e.g., :class:`from_dir` instead if you prefer to have these automatically generated from a directory of NEB calculations. Args: 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. """ if len(outcars) != len(structures): raise ValueError("# of Outcars must be same as # of Structures") # Calculate cumulative root mean square distance between structures, # which serves as the reaction coordinate. Note that these are # calculated from the final relaxed structures as the coordinates may # have changed from the initial interpolation. r = [0] prev = structures[0] for st in structures[1:]: dists = np.array([s2.distance(s1) for s1, s2 in zip(prev, st)]) r.append(np.sqrt(np.sum(dists ** 2))) prev = st r = np.cumsum(r) energies = [] forces = [] for i, o in enumerate(outcars): o.read_neb() energies.append(["energy"]) if i in [0, len(outcars) - 1]: forces.append(0) else: forces.append(["tangent_force"]) forces = np.array(forces) r = np.array(r) return cls(r=r, energies=energies, forces=forces, structures=structures, **kwargs)
[docs] def get_extrema(self, normalize_rxn_coordinate=True): """ Returns the positions of the extrema along the MEP. Both local minimums and maximums are returned. Args: 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), ...]. """ x = np.arange(0, np.max(self.r), 0.01) y = self.spline(x) * 1000 scale = 1 if not normalize_rxn_coordinate else 1 / self.r[-1] min_extrema = [] max_extrema = [] for i in range(1, len(x) - 1): if y[i] < y[i - 1] and y[i] < y[i + 1]: min_extrema.append((x[i] * scale, y[i])) elif y[i] > y[i - 1] and y[i] > y[i + 1]: max_extrema.append((x[i] * scale, y[i])) return min_extrema, max_extrema
[docs] def get_plot(self, normalize_rxn_coordinate=True, label_barrier=True): """ Returns the NEB plot. Uses Henkelman's approach of spline fitting each section of the reaction path based on tangent force and energies. Args: 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. """ plt = pretty_plot(12, 8) scale = 1 if not normalize_rxn_coordinate else 1 / self.r[-1] x = np.arange(0, np.max(self.r), 0.01) y = self.spline(x) * 1000 relative_energies = self.energies - self.energies[0] plt.plot(self.r * scale, relative_energies * 1000, 'ro', x * scale, y, 'k-', linewidth=2, markersize=10) plt.xlabel("Reaction coordinate") plt.ylabel("Energy (meV)") plt.ylim((np.min(y) - 10, np.max(y) * 1.02 + 20)) if label_barrier: data = zip(x * scale, y) barrier = max(data, key=lambda d: d[1]) plt.plot([0, barrier[0]], [barrier[1], barrier[1]], 'k--') plt.annotate('%.0f meV' % (np.max(y) - np.min(y)), xy=(barrier[0] / 2, barrier[1] * 1.02), xytext=(barrier[0] / 2, barrier[1] * 1.02), horizontalalignment='center') plt.tight_layout() return plt
[docs] @classmethod def from_dir(cls, root_dir, relaxation_dirs=None, **kwargs): """ 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 Args: 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. """ neb_dirs = [] for d in os.listdir(root_dir): pth = os.path.join(root_dir, d) if os.path.isdir(pth) and d.isdigit(): i = int(d) neb_dirs.append((i, pth)) neb_dirs = sorted(neb_dirs, key=lambda d: d[0]) outcars = [] structures = [] # Setup the search sequence for the OUTCARs for the terminal # directories. terminal_dirs = [] if relaxation_dirs is not None: terminal_dirs.append(relaxation_dirs) terminal_dirs.append((neb_dirs[0][1], neb_dirs[-1][1])) terminal_dirs.append([os.path.join(root_dir, d) for d in ["start", "end"]]) terminal_dirs.append([os.path.join(root_dir, d) for d in ["initial", "final"]]) for i, d in neb_dirs: outcar = glob.glob(os.path.join(d, "OUTCAR*")) contcar = glob.glob(os.path.join(d, "CONTCAR*")) poscar = glob.glob(os.path.join(d, "POSCAR*")) terminal = i == 0 or i == neb_dirs[-1][0] if terminal: for ds in terminal_dirs: od = ds[0] if i == 0 else ds[1] outcar = glob.glob(os.path.join(od, "OUTCAR*")) if outcar: outcar = sorted(outcar) outcars.append(Outcar(outcar[-1])) break else: raise ValueError("OUTCAR cannot be found for terminal " "point %s" % d) structures.append(Poscar.from_file(poscar[0]).structure) else: outcars.append(Outcar(outcar[0])) structures.append(Poscar.from_file(contcar[0]).structure) return NEBAnalysis.from_outcars(outcars, structures, **kwargs)
[docs] def as_dict(self): """ Dict representation of NEBAnalysis. Returns: JSON serializable dict representation. """ return {"@module": self.__class__.__module__, "@class": self.__class__.__name__, 'r': jsanitize(self.r), 'energies': jsanitize(self.energies), 'forces': jsanitize(self.forces), 'structures': [s.as_dict() for s in self.structures]}
[docs]def combine_neb_plots(neb_analyses, arranged_neb_analyses=False, reverse_plot=False): """ 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 """ x = StructureMatcher() for neb_index in range(len(neb_analyses)): if neb_index == 0: neb1 = neb_analyses[neb_index] neb1_energies = list(neb1.energies) neb1_structures = neb1.structures neb1_forces = neb1.forces neb1_r = neb1.r continue neb2 = neb_analyses[neb_index] neb2_energies = list(neb2.energies) matching = 0 for neb1_s in [neb1_structures[0], neb1_structures[-1]]: if, neb2.structures[0]) or \, neb2.structures[-1]): matching += 1 break if matching == 0: raise ValueError("no matched structures for connection!") neb1_start_e, neb1_end_e = neb1_energies[0], neb1_energies[-1] neb2_start_e, neb2_end_e = neb2_energies[0], neb2_energies[-1] min_e_diff = min(([abs(neb1_start_e - neb2_start_e), abs(neb1_start_e - neb2_end_e), abs(neb1_end_e - neb2_start_e), abs(neb1_end_e - neb2_end_e)])) if arranged_neb_analyses: neb1_energies = neb1_energies[0:len(neb1_energies) - 1] \ + [(neb1_energies[-1] + neb2_energies[0]) / 2] \ + neb2_energies[ 1:] neb1_structures = neb1_structures + neb2.structures[1:] neb1_forces = list(neb1_forces) + list(neb2.forces)[1:] neb1_r = list(neb1_r) + [i + neb1_r[-1] for i in list(neb2.r)[1:]] elif abs(neb1_start_e - neb2_start_e) == min_e_diff: neb1_energies = list(reversed(neb1_energies[1:])) + neb2_energies neb1_structures = list( reversed((neb1_structures[1:]))) + neb2.structures neb1_forces = list(reversed(list(neb1_forces)[1:])) + list( neb2.forces) neb1_r = list(reversed( [i * -1 - neb1_r[-1] * -1 for i in list(neb1_r)[1:]])) + [ i + neb1_r[-1] for i in list(neb2.r)] elif abs(neb1_start_e - neb2_end_e) == min_e_diff: neb1_energies = neb2_energies + neb1_energies[1:] neb1_structures = neb2.structures + neb1_structures[1:] neb1_forces = list(neb2.forces) + list(neb1_forces)[1:] neb1_r = [i for i in list(neb2.r)] + \ [i + list(neb2.r)[-1] for i in list(neb1_r)[1:]] elif abs(neb1_end_e - neb2_start_e) == min_e_diff: neb1_energies = neb1_energies + neb2_energies[1:] neb1_structures = neb1_structures + neb2.structures[1:] neb1_forces = list(neb1_forces) + list(neb2.forces)[1:] neb1_r = [i for i in list(neb1_r)] + [i + neb1_r[-1] for i in list(neb2.r)[1:]] else: neb1_energies = neb1_energies + list(reversed(neb2_energies))[1:] neb1_structures = neb1_structures + list( reversed((neb2.structures)))[1:] neb1_forces = list(neb1_forces) + list(reversed(list(neb2.forces)))[1:] neb1_r = list(neb1_r) + list( reversed([i * -1 - list(neb2.r)[-1] * -1 + list(neb1_r)[-1] for i in list(neb2.r)[:-1]])) if reverse_plot: na = NEBAnalysis( list(reversed([i * -1 - neb1_r[-1] * -1 for i in list(neb1_r)])), list(reversed(neb1_energies)), list(reversed(neb1_forces)), list(reversed(neb1_structures))) else: na = NEBAnalysis(neb1_r, neb1_energies, neb1_forces, neb1_structures) return na