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"""Demonstrates molecular dynamics with constant temperature."""
from asap3 import EMT # Way too slow with ase.EMT !
from ase import units
from ase.io.trajectory import Trajectory
from ase.lattice.cubic import FaceCenteredCubic
from ase.md.langevin import Langevin
size = 10
T = 1500 # Kelvin
# Set up a crystal
atoms = FaceCenteredCubic(
directions=[[1, 0, 0], [0, 1, 0], [0, 0, 1]],
symbol='Cu',
size=(size, size, size),
pbc=False,
)
# Describe the interatomic interactions with the Effective Medium Theory
atoms.calc = EMT()
# We want to run MD with constant energy using the Langevin algorithm
# with a time step of 5 fs, the temperature T and the friction
# coefficient to 0.02 atomic units.
dyn = Langevin(atoms, 5 * units.fs, T * units.kB, 0.002)
def printenergy(a=atoms): # store a reference to atoms in the definition.
"""Function to print the potential, kinetic and total energy."""
epot = a.get_potential_energy() / len(a)
ekin = a.get_kinetic_energy() / len(a)
print(
'Energy per atom: Epot = %.3feV Ekin = %.3feV (T=%3.0fK) '
'Etot = %.3feV' % (epot, ekin, ekin / (1.5 * units.kB), epot + ekin)
)
dyn.attach(printenergy, interval=50)
# We also want to save the positions of all atoms after every 100th time step.
traj = Trajectory('moldyn3.traj', 'w', atoms)
dyn.attach(traj.write, interval=50)
# Now run the dynamics
printenergy()
dyn.run(5000)
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