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])
#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)
print 'Completed energy optimization'
energy = sys.get_potential_energy()
print "Energy: %f" % energy
def relax(base_dir="./", model="A", smax=2e-4, fmax=0.05):
assert model.upper() in ("A", "B", "C")
curr_dir = os.path.dirname(os.path.abspath(__file__))
param_file = os.path.join(curr_dir, "params.json")
gpw_file = os.path.join(base_dir, "gs_{}.gpw".format(model.upper()))
traj_filename = os.path.join(base_dir,
"relax_{}.traj".format(model.upper()))
traj_fin_filename = os.path.join(base_dir,
"relax_fin_{}.traj".format(model.upper()))
# Trajectory file from previous relaxation
traj_base_filename = os.path.join(base_dir, "relaxed.traj")
old_traj_filename = os.path.join(base_dir,
"relax_{}.old.traj".format(model.upper()))
log_filename = os.path.join(base_dir, "relax_{}.log".format(model.upper()))
if os.path.exists(gpw_file):
parprint("Relaxation already done, will use gpw directly!")
return 0
if os.path.exists(param_file):
params = json.load(open(param_file, "r"))
else:
raise FileNotFoundError("no parameter file!")
# Perform relaxation process
# If has trajectory, use the last image
assert os.path.exists(traj_base_filename)
# Get stress for original structure
parprint("Calculate stress on original structure")
calc = GPAW(**params["relax"],
txt=os.path.join(base_dir, "gs.txt".format(model)))
atoms_origin = Trajectory(traj_base_filename)[-1]
atoms_origin.set_calculator(calc)
s = atoms_origin.get_stress()
parprint("Origin lattice, stress = ", s)
del atoms_origin, calc
# Now new calculations
if os.path.exists(old_traj_filename):
atoms = Trajectory(old_traj_filename)[-1]
else:
atoms = Trajectory(traj_base_filename)[-1]
for pos in model_dict[model]:
parprint("Add Na+ in position {}!".format(pos))
add_adatom(atoms, scaled_pos=pos)
view(atoms) # Should be safe for batch systems
# if os.path.exists(traj__filename):
# parprint("Relaxed, now calculated GS!")
# atoms = ase.io.read(traj_fin_filename)
# calc = GPAW(**params["gs"],
# txt=os.path.join(base_dir, "gs.txt"))
# atoms.set_calculator(calc)
# atoms.get_potential_energy()
# calc.write(gpw_file, mode="all")
# return
# else:
# if os.path.exists(old_traj_filename):
# try:
# t = Trajectory(old_traj_filename)
# atoms = t[-1] # use the last image
# parprint("Has trajectory file, use directly!")
# parprint("New atom position", atoms)
# except Exception as e:
# parprint("Trajectory file may be corrupted!")
world.barrier()
if model in ("A", "B"):
charge = 1
else:
charge = 2
calc = GPAW(**params["relax"],
charge=charge,
txt=os.path.join(base_dir, "relax_{}.txt".format(model)))
parprint(calc.parameters)
parprint("Init magmom", atoms.get_initial_magnetic_moments())
atoms.set_calculator(calc)
# optimizations
max_iter = 5
sf = StrainFilter(atoms)
# sf = ExpCellFilter(atoms)
# opt_unitcell = BFGS(sf,
# logfile=log_filename,
# trajectory=traj_filename)
# opt_unitcell.run(fmax=fmax)
# shutil.copyfile(traj_filename, old_traj_filename)
# for _ in range(max_iter):
for i in range(max_iter):
opt_cell = BFGS(sf, logfile=log_filename, trajectory=traj_filename)
opt_norm = BFGS(atoms, logfile=log_filename, trajectory=traj_filename)
opt_norm.run(fmax=fmax)
s = atoms.get_stress()
parprint("Cycle {}, Addition stress {}".format(i, s))
opt_cell.run(fmax=fmax)
# shutil.copyfile(traj_filename, old_traj_filename)
# opt_cell.run(fmax=fmax)
atoms.write(traj_fin_filename)
# calc.set(**params["gs"],
# txt=os.path.join(base_dir,
# "gs.txt"))
# atoms.get_potential_energy()
# calc.write(gpw_file, mode="all")
return True
