atoms.set_momenta(1e-6 * random.random([len(atoms), 3]))
print "Initializing ..."
predyn = VelocityVerlet(atoms, 0.5)
try:
predyn.run(2500)
except:
print atoms.arrays['positions']
print atoms.arrays['momenta']
print atoms.arrays['momenta'].shape
print atoms.get_masses()
print atoms.get_masses().shape
raise
initr = atoms.get_positions()
initp = atoms.get_momenta()
def targetfunc(params, x):
return params[0] * exp(-params[1] * x) + params[2]
output = file("Langevin.dat", "w")
for temp, frict in ((0.01, 0.001),):
dyn = Langevin(atoms, timestep, temp, frict)
print ""
print "Testing Langevin dynamics with T = %f eV and lambda = %f" % (temp, frict)
ekin = atoms.get_kinetic_energy()/natoms
print ekin
output.write("%.8f\n" % ekin)
temperatures = [(0, 2.0 / 3.0 * ekin)]
