for k in range(N):
pos.append((i, j, k))
pos.append((i, j + 0.5, k + 0.5))
pos.append((i + 0.5, j, k + 0.5))
pos.append((i + 0.5, j + 0.5, k))
pos = array(pos) * latconst
supercell = [N * latconst, N * latconst, N * latconst]
# Create the atoms object
atoms = ListOfAtoms(positions=pos, cell=supercell)
atoms.SetAtomicNumbers(Z)
# The dynamics
atoms.SetCalculator(EMT()) # Use the EMT potential
dyn = Langevin(atoms, 5 * femtosecond, 800 * kB, 0.002)
# Output to NetCDF file
trajectory = NetCDFTrajectory("output.nc", atoms, interval=2000)
dyn.Attach(trajectory)
# Do the dynamics
for i in range(100):
if i == 50:
dyn.SetTemperature(2000 * kB)
print "Setting temperature to 2000K"
dyn.Run(100)
print "Ekin = %.5f Epot = %.5f Etot = %.5f" % \
(atoms.GetKineticEnergy()/len(atoms),
atoms.GetPotentialEnergy()/len(atoms),
(atoms.GetKineticEnergy()+atoms.GetPotentialEnergy())/len(atoms))
cna.Attach(plotter)
# We output and plot the instantaneous positions. Replace atoms with
# avg to output and plot the averaged positions instead.
plotter = FieldPlotter(atoms, atoms.GetTags, verbose=1)
plotter.SetBlackWhiteColors(reverse=True)
plotter.SetDataRange('plot')
plotter.SetOutput(PostScriptFile("bwplot"))
plotter.SetOutput(GifFile("bwplot"))
plotter.SetLog(plotlog)
cna.Attach(plotter)
# Run the simulation
dyn.Run(n_total)
plotlog.close()
if cleanup:
print "Removing output files"
print "Deleting plot.log"
os.unlink("plot.log")
for name in ("cna_plot", "fieldplot", "bwplot"):
for num in ("0000", "0001"):
for ending in (".ps", ".gif"):
fn = name + num + ending
print "Deleting", fn
os.unlink(fn)
print
dyn = Langevin(atoms, dt=5*femtosecond, temperature=800*kB, friction=0.005)
# Make a trajectory
traj = NetCDFTrajectory('MD_Cluster.nc', atoms, interval=500)
dyn.Attach(traj)
# Write the initial configuration
traj.Update()
# Print the energies
def printenergy(a, step=[0,]):
n = len(a)
ekin = a.GetKineticEnergy() / n
epot = a.GetPotentialEnergy() / n
print ("%4d: E_kin = %-9.5f E_pot = %-9.5f E_tot = %-9.5f T = %.1f K" %
(step[0], ekin, epot, ekin+epot, 2.0/3.0*ekin/kB))
step[0] += 1
printenergy(atoms)
# Now do the dynamics, doing 5000 timesteps, writing energies every 50 steps
for major in range(100):
dyn.Run(50)
printenergy(atoms)
# Now increase the temperature to 2000 K and continue
dyn.SetTemperature(2000 * kB)
for major in range(100):
dyn.Run(50)
printenergy(atoms)