file_name = file_name_py.replace('.py', '')
file_traj = file_name + '.traj'
start_file = '../In2O3_110_clean.traj'
mode = 'a'
try:
sys = Trajectory(file_traj, 'r')[-1]
except (IOError, RuntimeError):
print "Importing trajectory file from: %s" % start_file
sys = read(start_file)
sys.center(vacuum=5.0, axis=2)
else:
print "Importing trajectory file from: %s" % file_traj
set_calc_In2O3(sys)
print "Constraints:"
print " c1: Fix bottom two layers."
avg_z = np.mean([atom.z for atom in sys])
c1 = FixAtoms(mask=[atom.z < avg_z for atom in sys])
sys.set_constraint(c1)
if testRun == True:
run_testRun(sys)
else:
geo_traj = Trajectory(file_traj, mode, sys)
dyn = LBFGS(sys, trajectory=geo_traj)
dyn.run(fmax=0.05)
energy = sys.get_potential_energy()
print "Energy: %f" % energy
print "Completed %s" % file_name_py
# In[10]:
atom2 = read('c2h6.gen')
ao2 = AtomOP(atom2)
# pairs = [[1,2],[13,7],[5,26]]
pairs = [[0, 1]]
images2 = ao2.stretch(pairs, nbin=50, wtraj=True)
ao2.close()
view(images2)
# In[14]:
e_c2h4, e_c2h6 = [], []
for atoms in images:
e_c2h4.append(atoms.get_potential_energy())
for atoms in images2:
e_c2h6.append(atoms.get_potential_energy())
fig, ax = plt.subplots()
plt.plot(e_c2h4[0:40] - min(e_c2h4),
label=r'$C_{2}H_4$',
color='blue',
linewidth=2,
linestyle='-.')
plt.plot(e_c2h6[0:40] - min(e_c2h6),
label=r'$C_{2}H_6$',
color='r',
linewidth=2,
linestyle='-')
plt.legend(loc='best', edgecolor='yellowgreen')
