ASE Manual Release 3.6.1.2825 CAMd - CampOS Wiki

atoms.set_calculator(EMT())
# Set the momenta corresponding to T=300K
MaxwellBoltzmannDistribution(atoms, 300*units.kB)
ASE Manual, Release 3.6.1.2828
# We want to run MD with constant energy using the VelocityVerlet algorithm.
dyn = VelocityVerlet(atoms, 5*units.fs) # 5 fs time step.
#Function to print the potential, kinetic and total energy
def printenergy(a):
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))
# Now run the dynamics
printenergy(atoms)
for i in range(20):
dyn.run(10)
printenergy(atoms)
Note how the total energy is conserved, but the kinetic energy quickly drops to half the expected value. Why?
Instead of printing within a loop, it is possible to use an “observer” to observe the atoms and do the printing (or
more sophisticated analysis).
"Demonstrates molecular dynamics with constant energy."
from ase.calculators.emt import EMT
from ase.lattice.cubic import FaceCenteredCubic
from ase.md.velocitydistribution import MaxwellBoltzmannDistribution
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 = 10
else:
size = 3
# Set up a crystal
atoms = FaceCenteredCubic(directions=[[1,0,0],[0,1,0],[0,0,1]], symbol="Cu",
size=(size,size,size), pbc=True)
# Describe the interatomic interactions with the Effective Medium Theory
atoms.set_calculator(EMT())
# Set the momenta corresponding to T=300K
MaxwellBoltzmannDistribution(atoms, 300*units.kB)
# We want to run MD with constant energy using the VelocityVerlet algorithm.
dyn = VelocityVerlet(atoms, 5*units.fs) # 5 fs time step.
#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))
6.2. ASE 39