plotNEB.py

#!/usr/bin/env python
""" NEB plotter.

This script plots the NEB spline obtained from a VTST Tools NEB calculation.
The data is obtained from the nebef.dat file.

Author: Uthpala Herath

Usage:
plotNEB.py -n 29

"""

from scipy.interpolate import interp1d
import numpy as np
import matplotlib.pyplot as plt
import argparse

def plot_NEB(natoms=1):
    """ This method plots a spline for the NEB obtained from the
    nebef.dat file generated by VTST tools."""

    # Open nebef.dat
    fi = open("nebef.dat","r")
    data = fi.readlines()
    fi.close()

    # save energy in list
    y_dft = [float(i.split()[2]) for i in data]
    x = np.arange(0, len(y_dft))
    y_dft = np.array(y_dft)

    # normalizing and shifting
    y_dft = (y_dft - y_dft[0]) / natoms

    # spline
    f_dft = interp1d(x, y_dft, kind="cubic")

    xnew = np.linspace(0, len(y_dft)-1, num=100, endpoint=True)

    # plotting
    plt.figure(figsize=(13, 9))

    plt.plot(x, y_dft, "mo", label="Raw NEB points")
    plt.plot(xnew, f_dft(xnew), "m-", label="Interpolated NEB")

    plt.axhline(color="black", linestyle="--")
    plt.xlabel("Reaction coordinate")
    plt.ylabel("Energy (eV/atom)")

    plt.legend(loc="best")
    plt.grid(color="gainsboro", ls="--", lw=0.6)
    plt.title("NEB")
    plt.savefig("NEB.pdf")
    #plt.show()

if __name__ == "__main__":
    parser = argparse.ArgumentParser(description=__doc__)
    parser.add_argument("-n","--natoms", type=int, help="Number of atoms",default=1)
    args = parser.parse_args()
    plot_NEB(args.natoms)