ASE Manual Release 3.6.1.2825 CAMd - CampOS Wiki

ag moldyn3.traj
ASE Manual, Release 3.6.1.2828
Try plotting the kinetic energy. You will not see a well-defined melting point due to finite size effects (including
surface melting), but you will probably see an almost flat region where the inside of the system melts. The
outermost layers melt at a lower temperature.
Note: The Langevin dynamics will by default keep the position and momentum of the center of mass unperturbed.
This is another improvement over just setting momenta corresponding to a temperature, as we did before.
Isolated particle MD
When simulating isolated particles with MD, it is sometimes preferable to set random momenta corresponding to
a spefic temperature and let the system evolve freely. With a relatively high temperature, the is however a risk that
the collection of atoms will drift out of the simulation box because the randomized momenta gave the center of
mass a small but non-zero velocity too.
Let us see what happens when we propagate a nanoparticle for a long time:
"Demonstrates molecular dynamics for isolated particles."
from ase.calculators.emt import EMT
from ase.cluster.cubic import FaceCenteredCubic
from ase.optimize import QuasiNewton
from ase.md.velocitydistribution import MaxwellBoltzmannDistribution, \
Stationary, ZeroRotation
from ase.md.verlet import VelocityVerlet
from ase import units
# Use Asap for a huge performance increase if it is installed
useAsap = True
if useAsap:
from asap3 import EMT
size = 4
else:
size = 2
# Set up a nanoparticle
atoms = FaceCenteredCubic(’Cu’, surfaces=[[1,0,0],[1,1,0],[1,1,1]],
layers=(size,size,size), vacuum=4)
# Describe the interatomic interactions with the Effective Medium Theory
atoms.set_calculator(EMT())
# Do a quick relaxation of the cluster
qn = QuasiNewton(atoms)
qn.run(0.001, 10)
# Set the momenta corresponding to T=1200K
MaxwellBoltzmannDistribution(atoms, 1200*units.kB)
Stationary(atoms) # zero linear momentum
ZeroRotation(atoms) # zero angular momentum
# We want to run MD using the VelocityVerlet algorithm.
dyn = VelocityVerlet(atoms, 5*units.fs, trajectory=’moldyn4.traj’) # save trajectory.
#Function to print the potential, kinetic and total energy.
def printenergy(a=atoms): #store a reference to atoms in the definition.
epot = a.get_potential_energy() / len(a)
ekin = a.get_kinetic_energy() / len(a)
6.2. ASE 41