#dp = np.sqrt(2 * a.mass * 1000.0)
#a.momentum = np.array([0, 0, dp])
t = np.zeros(len(atoms), int)
t[n] = 1
atoms.set_tags(t)
else:
atoms = None
atoms = MakeParallelAtoms(atoms, cpulayout)
print len(atoms), atoms.get_number_of_atoms()
atoms.set_calculator(EMT())
traj = PickleTrajectory("UnBalance.traj", "w", atoms)
if fast:
atoms.get_forces()
traj.write()
for i in range(50):
print "\n\n\n\n*** STEP %i ***\n\n\n\n\n" % (i, )
r = atoms.get_positions()
r += atoms.get_tags().reshape((-1, 1)) * np.array([
[0, 0, 20.0],
])
atoms.set_positions(r)
atoms.get_forces()
traj.write()
else:
dyn = VelocityVerlet(atoms, 5 * units.fs)
logger = MDLogger(dyn, atoms, 'UnBalance.log', stress=True, peratom=True)
dyn.attach(logger, interval=10)
dyn.attach(traj, interval=100)
dyn.run(10000)
#dp = np.sqrt(2 * a.mass * 1000.0)
#a.momentum = np.array([0, 0, dp])
t = np.zeros(len(atoms), int)
t[n] = 1
atoms.set_tags(t)
else:
atoms = None
atoms = MakeParallelAtoms(atoms, cpulayout)
print len(atoms), atoms.get_number_of_atoms()
atoms.set_calculator(EMT())
traj = PickleTrajectory("UnBalance.traj", "w", atoms)
if fast:
atoms.get_forces()
traj.write()
for i in range(50):
print "\n\n\n\n*** STEP %i ***\n\n\n\n\n" % (i,)
r = atoms.get_positions()
r += atoms.get_tags().reshape((-1,1)) * np.array([[0, 0, 20.0],])
atoms.set_positions(r)
atoms.get_forces()
traj.write()
else:
dyn = VelocityVerlet(atoms, 5*units.fs)
logger = MDLogger(dyn, atoms, 'UnBalance.log', stress=True, peratom=True)
dyn.attach(logger, interval=10)
dyn.attach(traj, interval=100)
dyn.run(10000)
