# The plotter
def invisible_atoms(a):
"""Return True for atoms that should be invisible."""
r = atoms.get_positions()
centerofmass = r.sum(axis=0) / len(atoms)
return (r[:,2] < centerofmass[2])
plotter = PrimiPlotter(atoms)
plotter.set_invisibility_function(invisible_atoms)
plotter.set_colors(mycolors) # Map tags to colors
# plotter.set_output(X11Window()) # Plot in a window on the screen
plotter.set_output(JpegFile("ptm")) # Save plots in files plt0000.gif ...
plotter.set_rotation((10.0, 5.0, 0))
# Attach the plotter to the PTMobserver object. That guarantees
# that the plotter is called AFTER the PTM analysis has been done.
# Similarly, a Trajectory should be attached to the PTMobserver
# object. By using interval=1 (the default), the plotter is called
# every time PTMobserver is called, i.e. every plotinterval
# timesteps.
ptm.attach(plotter.plot)
# The main loop
for t in temperatures:
dyn.set_temperature(units.kB*t)
for i in range(nsteps/100):
dyn.run(100)
print "E_total = %-10.5f T = %.0f K (goal: %.0f K, step %d of %d)" %\
(atoms.get_total_energy()/len(atoms), atoms.get_temperature(), t, i, nsteps/100)
# Associate the EMT potential with the atoms
atoms.set_calculator(EMT())
# Temperature profile
temperatures = (250, 500, 750, 1000, 1250, 1500, 1750)
# How many steps at each temperature
nsteps = 10000
# Interval between plots
plotinterval = 2000
# Make the Langevin dynamics module
dyn = Langevin(atoms, 5 * units.fs, units.kB * temperatures[0], 0.002)
# The plotter
plotter = PrimiPlotter(atoms)
# plotter.set_output(X11Window()) # Plot in a window on the screen
plotter.set_output(PngFile("plt")) # Save plots in files plt0000.gif ...
plotter.set_rotation((10.0, 5.0, 0))
dyn.attach(plotter.plot, interval=plotinterval)
# The main loop
for t in temperatures:
dyn.set_temperature(units.kB * t)
for i in range(nsteps // 100):
dyn.run(100)
print("E_total = %-10.5f T = %.0f K (goal: %.0f K, step %d of %d)" %\
(atoms.get_total_energy()/len(atoms), atoms.get_temperature(),
t, i, nsteps//100))
