matplotlib example ChemOrder GA Animate (snippet)

Python matplotlib example 'ChemOrder GA Animate'

Modules used in program:

• import matplotlib.cm as cm
• import matplotlib.pyplot as plt
• import matplotlib
• import subprocess
• import numpy as np

python ChemOrder GA Animate

Python matplotlib example: ChemOrder GA Animate

"""Animate results from a GA search for chemical ordering optimization in
nanoparticles. Assumes http://www.imagemagick.org/ has been installed."""
import numpy as np
import subprocess
import matplotlib
import matplotlib.pyplot as plt
import matplotlib.cm as cm

from ase.db import connect

matplotlib.rc('font', serif='Helvetica Neue Light')
matplotlib.rcParams.update({'font.size': 22})

db = connect('gadb.db')

energy = []
mass = []
index = []
i = 0
for row in db.select(relaxed=True):
    i += 1
    c = row.toatoms(add_additional_information=True)
    energy.append(c.info['key_value_pairs']['raw_score'] * -1.)
    mass.append(round(sum(c.get_masses()), 2))
    index.append(i)

cenergy, cmass, cindex = [], [], []
fname = []
for i in range(len(index)):
    cenergy.append(energy[i])
    cmass.append(mass[i])
    cindex.append(index[i])

    fig = plt.figure(figsize=(12, 12))
    ax = fig.add_subplot(111)
    ax.axis([min(mass)-10, max(mass)+10, -5.5, 5.5])
    ax.scatter(cmass, cenergy, c=cindex, cmap=cm.rainbow, alpha=0.5)
    plt.xlabel('Mass')
    plt.ylabel('Stability (eV)')

    n = 'images/{0}_gaPtAu.png'.format(i)
    fname.append(n)
    fig.savefig(n)

call = 'convert -delay 15 -loop 0 '
for i in fname:
    call += i + ' '
call += 'images/animated.gif'

subprocess.call(call, shell=True)

Python links

• Learn Python: https://pythonbasics.org/
• Python Tutorial: https://pythonprogramminglanguage.com