atoms.center(vacuum=10.0, axis=2)
atoms.set_momenta(np.zeros((len(atoms), 3)))
# Select an atom to get a kick
r = atoms.get_positions()
uc = atoms.get_cell()
x = r[:, 0] - 0.5 * uc[0, 0]
y = r[:, 1] - 0.5 * uc[1, 1]
z = r[:, 2]
zprime = z - 0.01 * (x * x + y * y)
n = np.argmax(zprime)
#a = atoms[n]
#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],
if world.size == 1:
cpulayout = None
elif world.size == 2:
cpulayout = [2,1,1]
elif world.size == 3:
cpulayout = [1,3,1]
elif world.size == 4:
cpulayout = [2,1,2]
if ismaster:
init = FaceCenteredCubic(size=(10,10,10), symbol='Cu', pbc=False)
z = init.get_positions()[:,2]
fixedatoms = np.less(z, 0.501*z.max())
print len(init), sum(fixedatoms)
MaxwellBoltzmannDistribution(init, 6000*units.kB)
init.set_tags(fixedatoms)
else:
init = None
print
print "Running simulation with Filter"
atoms1 = MakeParallelAtoms(init, cpulayout)
atoms1.arrays['r_init'] = atoms1.get_positions()
atoms1.set_calculator(EMT())
atoms1a = Filter(atoms1, mask=np.logical_not(atoms1.get_tags()))
dyn = VelocityVerlet(atoms1a, 3*units.fs)
dyn.run(100)
print
print "Running simulation with Asap's FixAtoms"
atoms.center(vacuum=10.0, axis=2)
atoms.set_momenta(np.zeros((len(atoms),3)))
# Select an atom to get a kick
r = atoms.get_positions()
uc = atoms.get_cell()
x = r[:,0] - 0.5 * uc[0,0]
y = r[:,1] - 0.5 * uc[1,1]
z = r[:,2]
zprime = z - 0.01 * (x * x + y * y)
n = np.argmax(zprime)
#a = atoms[n]
#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)
