def test_replay():
from math import sqrt
from ase import Atoms, Atom
from ase.constraints import FixAtoms
from ase.calculators.emt import EMT
from ase.optimize import QuasiNewton
from ase.io import read
from ase.visualize import view
# Distance between Cu atoms on a (100) surface:
d = 3.6 / sqrt(2)
a = Atoms('Cu',
positions=[(0, 0, 0)],
cell=(d, d, 1.0),
pbc=(True, True, False))
a *= (2, 2, 1) # 2x2 (100) surface-cell
# Approximate height of Ag atom on Cu(100) surfece:
h0 = 2.0
a += Atom('Ag', (d / 2, d / 2, h0))
if 0:
view(a)
constraint = FixAtoms(range(len(a) - 1))
a.calc = EMT()
a.set_constraint(constraint)
dyn1 = QuasiNewton(a, trajectory='AgCu1.traj', logfile='AgCu1.log')
dyn1.run(fmax=0.1)
a = read('AgCu1.traj')
a.calc = EMT()
print(a.constraints)
dyn2 = QuasiNewton(a, trajectory='AgCu2.traj', logfile='AgCu2.log')
dyn2.replay_trajectory('AgCu1.traj')
dyn2.run(fmax=0.01)
'a').write("Run %i ended on " % (run) +
time.strftime('%m/%d/%Y\t%H:%M:%S') +
" after %4.2f hours" %
((now - starttime) / 3600.) + '\n')
os.system(restart_command)
sys.exit()
####################################
qn.attach(traj)
qn.attach(StopCalc)
starttime = time.time()
if run > 0:
qn.replay_trajectory('qn.traj')
qn.run(fmax=0.05)
pdos.pdos(atoms,
outdir='outdir',
spinpol=False,
save_pkl=save_pdos_pkl,
Emin=-20,
Emax=20,
kpts=(kpts[0] * 3, kpts[1] * 3, 1),
DeltaE=0.01,
nscf=True)
bader.bader(atoms,
outdir='outdir',
spinpol=False,
from ase.io import read
from ase.vibrations import Vibrations
# Distance between Cu atoms on a (100) surface:
d = 3.6 / sqrt(2)
a = Atoms('Cu',
positions=[(0, 0, 0)],
cell=(d, d, 1.0),
pbc=(True, True, False))
a *= (2, 2, 1) # 2x2 (100) surface-cell
# Approximate height of Ag atom on Cu(100) surfece:
h0 = 2.0
a += Atom('Ag', (d / 2, d / 2, h0))
if 0:
view(a)
constraint = FixAtoms(range(len(a) - 1))
a.set_calculator(EMT())
a.set_constraint(constraint)
dyn1 = QuasiNewton(a, trajectory='AgCu1.traj', logfile='AgCu1.log')
dyn1.run(fmax=0.1)
a = read('AgCu1.traj')
a.set_calculator(EMT())
print a.constraints
dyn2 = QuasiNewton(a, trajectory='AgCu2.traj', logfile='AgCu2.log')
dyn2.replay_trajectory('AgCu1.traj')
dyn2.run(fmax=0.01)
