def Compare(name, atoms, observer, ref, interval=4):
dyn = VelocityVerlet(atoms, 5*units.fs)
dyn.attach(observer, interval=interval)
r = []
for i in range(50):
dyn.run(5)
epot = atoms.get_potential_energy() / len(atoms)
ekin = atoms.get_kinetic_energy() / len(atoms)
r.append([epot, ekin, epot+ekin])
r = array(r)
diff = r - ref
maxdiff = diff.max()
print "Maximal difference is", maxdiff
ReportTest(name, maxdiff, 0.0, 1e-6)
print "Number of atoms:", nTotalAtoms
epot = atoms.get_potential_energy() / nTotalAtoms
ekin = atoms.get_kinetic_energy() / nTotalAtoms
etotallist = [epot+ekin]
ekinlist = [ekin]
#report()
if ismaster:
print "\nE_pot = %-12.5f E_kin = %-12.5f E_tot = %-12.5f" % (epot, ekin,
epot+ekin)
ReportTest("Initial potential energy", epot,-3.4669, 1e-4)
ReportTest("Initial kinetic energy", ekin, 0.0, 1e-9)
dyn.attach(MDLogger(dyn, atoms, "-", peratom=True), interval=10)
for i in range(40):
dyn.run(10)
epot = atoms.get_potential_energy() / nTotalAtoms
ekin = atoms.get_kinetic_energy() / nTotalAtoms
etotallist.append(epot+ekin)
ekinlist.append(ekin)
if ismaster:
print "Average total energy:", sum(etotallist)/len(etotallist)
print "Average kinetic energy:", sum(ekinlist)/len(ekinlist)
ReportTest("Agv. total energy", sum(etotallist)/len(etotallist), -3.4669,
0.0001)
ReportTest("Agv. kinetic energy", sum(ekinlist)/len(ekinlist), 0.02165,
"""
from numpy import *
from asap3 import Atoms, EMT, units, Trajectory
from ase.lattice.cubic import FaceCenteredCubic
from asap3.md.verlet import VelocityVerlet
# Create the atoms
atoms = FaceCenteredCubic(size=(3, 3, 3), symbol="Cu", pbc=False)
# Give the first atom a non-zero momentum
atoms[0].momentum = array([0, -11.3, 0])
# Associate the EMT potential with the atoms
atoms.set_calculator(EMT())
# Now do molecular dynamics, printing kinetic, potential and total
# energy every ten timesteps.
dyn = VelocityVerlet(atoms, 5.0 * units.fs)
# Make a trajectory writing output
trajectory = Trajectory("TrajectoryMD-output.traj", "w", atoms)
# Attach it to the dynamics, so it is informed every fifth time a
# timestep is made.
dyn.attach(trajectory, interval=5)
# Now do 1000 timesteps.
dyn.run(1000)
print "The output is in the ASE Trajectory file TrajectoryMD-output.traj"
from numpy import * from asap3 import Atoms, EMT, units from ase.visualize.primiplotter import * from ase.lattice.cubic import FaceCenteredCubic from asap3.md.verlet import VelocityVerlet # Create the atoms atoms = FaceCenteredCubic(size=(3,3,3), symbol="Cu", pbc=False) # Give the first atom a non-zero momentum atoms[0].set_momentum(array([0, -11.3, 0])) # Associate the EMT potential with the atoms atoms.set_calculator(EMT()) # Now do molecular dynamics, printing kinetic, potential and total # energy every ten timesteps. dyn = VelocityVerlet(atoms, 5.0*units.fs) # Set up a plotter plotter = PrimiPlotter(atoms) plotter.set_output(X11Window()) # Attach it to the dynamics, so it is informed every 25'th time a # timestep is made. dyn.attach(plotter.plot, interval=25) # Now do 1000 timesteps. dyn.run(1000) print "The output is in the NetCDF file TrajectoryMD-output.traj"
from ase.visualize.primiplotter import *
from ase.lattice.cubic import FaceCenteredCubic
from asap3.md.verlet import VelocityVerlet
# Create the atoms
atoms = FaceCenteredCubic(size=(3,3,3), symbol="Cu", pbc=False)
# Give the first atom a non-zero momentum
atoms[0].momentum = array([0, -11.3, 0])
# Associate the EMT potential with the atoms
atoms.set_calculator(EMT())
# Now do molecular dynamics, printing kinetic, potential and total
# energy every ten timesteps.
dyn = VelocityVerlet(atoms, 5.0*units.fs)
# Set up a plotter
plotter = PrimiPlotter(atoms)
plotter.set_output(X11Window()) # Plot in X11 window on the user's screen
plotter.set_output(JpegFile("a")) # Save as GIF files
# plotter.set_output(PostScriptFile("a")) # Save as PS files
# Attach it to the dynamics, so it is informed every 25'th time a
# timestep is made.
dyn.attach(plotter.plot, interval=25)
# Now do 1000 timesteps.
dyn.run(1000)
print "The output is in the NetCDF file TrajectoryMD-output.traj"
from numpy import *
from asap3 import Atoms, EMT, units, PickleTrajectory
from ase.lattice.cubic import FaceCenteredCubic
from asap3.md.verlet import VelocityVerlet
# Create the atoms
atoms = FaceCenteredCubic(size=(3,3,3), symbol="Cu", pbc=False)
# Give the first atom a non-zero momentum
atoms[0].set_momentum(array([0, -11.3, 0]))
# Associate the EMT potential with the atoms
atoms.set_calculator(EMT())
# Now do molecular dynamics, printing kinetic, potential and total
# energy every ten timesteps.
dyn = VelocityVerlet(atoms, 5.0*units.fs)
# Make a trajectory writing output
trajectory = PickleTrajectory("TrajectoryMD-output.traj", "w", atoms)
# Attach it to the dynamics, so it is informed every fifth time a
# timestep is made.
dyn.attach(trajectory, interval=5)
# Now do 1000 timesteps.
dyn.run(1000)
print "The output is in the NetCDF file TrajectoryMD-output.traj"