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
file_traj = file_name + '.traj'
start_file = '../In2O3_110_H-1.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)
mode = 'w'
else:
print(("Importing trajectory file from: %s" % file_traj))
set_bader_calc(sys, sigma = 0.05)
print("Constraints:")
print(" c: Fix bottom two layers.")
c = FixAtoms(mask=[atom.z < 8 for atom in sys])
sys.set_constraint(c)
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('Generating CHGCAR_sum for Bader analysis...')
system('chgsum.pl AECCAR0 AECCAR2')
print('Performing Bader analysis (bader CHGCAR -ref CHGCAR_sum)')
system('bader CHGCAR -ref CHGCAR_sum')
print(('Completed %s' % file_name_py))
