ASE Manual Release 3.6.1.2825 CAMd - CampOS Wiki

ASE Manual, Release 3.6.1.2828
# Now run the dynamics
dyn.attach(printenergy, interval=10)
printenergy()
dyn.run(200)
Constant temperature MD
Often, you want to control the temperature of an MD simulation. This can be done with the Langevin dynamics
module. In the previous examples, replace the line dyn = VelocityVerlet(...) with:
dyn = Langevin(atoms, 5*units.fs, T*units.kB, 0.002)
where T is the desired temperature in Kelvin. You also need to import Langevin, see the class below.
The Langevin dynamics will then slowly adjust the total energy of the system so the temperature approaches the
desired one.
As a slightly less boring example, let us use this to melt a chunck of copper by starting the simulation without any
momentum of the atoms (no kinetic energy), and with a desired temperature above the melting point. We will also
save information about the atoms in a trajectory file called moldyn3.traj.
"Demonstrates molecular dynamics with constant energy."
from ase.calculators.emt import EMT
from ase.lattice.cubic import FaceCenteredCubic
from ase.md.langevin import Langevin
from ase.io.trajectory import PickleTrajectory
from ase import units
from asap3 import EMT # Way too slow with ase.EMT !
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.set_calculator(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)
#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)
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 = PickleTrajectory("moldyn3.traj", ’w’, atoms)
dyn.attach(traj.write, interval=50)
# Now run the dynamics
printenergy()
dyn.run(5000)
After running the simulation, you can study the result with the command
40 Chapter 6. Tutorials