from run_testRun import run_testRun
from set_calc import set_calc_In2O3
testRun = False
file_name_py = basename(__file__)
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)
from py_box.ase.set_calc import print_vasp_param, calc_dict, handle_restart
testRun = False
file_name_py = basename(__file__)
file_name = file_name_py.replace('.py', '')
file_traj = file_name + '.traj'
file_out = file_name + '.out'
mode = 'a'
try:
sys = Trajectory(file_traj, 'r')[-1]
except (IOError, RuntimeError):
print "Creating molecule from scratch"
sys = molecule('H2')
sys.set_cell(np.array([20, 21, 22]))
sys.center()
#sys *= (2, 3, 1)
else:
print "Importing trajectory file from: %s" % file_traj
vasp_param = calc_dict['TiO2_step']
vasp_param['kpts'] = (1, 1, 1)
calc = Vasp(**vasp_param)
handle_restart(calc, sys)
print_vasp_param(calc)
sys.set_calculator(calc)
del sys.constraints
#print 'Constraints:'
#print '\tc1: Freezing bottom two layers (z < 15.)'
#c1 = FixAtoms(mask = [atom.z < 15 for atom in sys])
