periodic=(0, 0, 1))
basis = atoms.GetUnitCell()
center = 0.5 * array([basis[0, 0], basis[1, 1], basis[2, 2]]) + array(
[0.1, 0.1, 0.1])
disl = Dislocation(center, atoms.MillerToDirection((1, 1, 0)),
atoms.MillerToDirection((1, 1, 0)) / 2.0)
#atoms = ListOfAtoms(slab)
disl.ApplyTo(atoms)
atoms.SetCalculator(EMT(EMTRasmussenParameters()))
# Constant temperatur dynamics
dyn = Langevin(atoms, 5 * femtosecond, 300 * kB, 0.002)
# Run Common Neighbor Analysis on each n_output timestep, using the
# positions averaged over the last n_avg timesteps, and writing the
# result to the output file.
avg = TimeAveragedPositions(atoms, n_avg, n_output)
dyn.Attach(avg)
cna = RestrictedCNA(avg, verbose=1)
avg.Attach(cna)
# We output and plot the instantaneous positions. Replace atoms with
# avg to output and plot the averaged positions instead.
plotlog = open("plot.log", "w")
plotter = PrimiPlotter(atoms, verbose=1)
plotter.SetOutput(PostScriptFile("cna_plot"))
plotter.SetOutput(GifFile("cna_plot"))
dynamics = VelocityVerlet(atoms, 5*femtosecond)
print "Running Verlet dynamics."
startcpu, startwall = time.clock(), time.time()
dynamics.Run(timesteps)
vpcpu, vpwall = time.clock() - startcpu, time.time() - startwall
vpfraction = vpcpu/vpwall
sys.stderr.write("\n")
print "Verlet dynamics done."
del dynamics, atoms
print "Preparing to run Langevin dynamics (periodic boundaries)."
atoms = ListOfAtoms(initial, periodic=(1,1,1))
atoms.SetCalculator(EMT())
dynamics = Langevin(atoms, 5*femtosecond, 400*kB, 0.001)
print "Running Langevin dynamics."
startcpu, startwall = time.clock(), time.time()
dynamics.Run(timesteps)
lcpu, lwall = time.clock() - startcpu, time.time() - startwall
lfraction = lcpu/lwall
sys.stderr.write("\n")
print "Langevin dynamics done."
del dynamics, atoms
print ""
print ""
print "TIMING RESULTS:"
print "Verlet (free): CPU time %.2fs Wall clock time %.2fs (%.0f%%)" % (vfcpu, vfwall, vffraction * 100)
min(rs) >= 0.0,
silent=True)
ReportTest.BoolTest("Overflow (%d)" % (self.n, ),
max(rs) <= 1.0,
silent=True)
print "Ekin =", atoms.GetKineticEnergy() / len(atoms), min(rs), max(rs)
PrintVersion(1)
atoms = FaceCenteredCubic(directions=[[1, 0, 0], [0, 1, 0], [0, 0, 1]],
size=(20, 10, 4),
element='Cu',
periodic=(1, 1, 1))
atoms.SetCalculator(EMT())
dyn = Langevin(atoms, 5 * femtosecond, 3000 * kB, 0.05)
dyn.Attach(Check(atoms))
dyn.Run(100)
r = matrixmultiply(atoms.GetCartesianPositions(),
inverse(atoms.GetUnitCell())).flat
print min(r), max(r)
atoms2 = ListOfAtoms(atoms)
atoms2.SetCartesianPositions(2 * atoms2.GetCartesianPositions() - 4.0)
atoms2.SetCalculator(EMT())
r = matrixmultiply(atoms2.GetCartesianPositions(),
inverse(atoms2.GetUnitCell())).flat
print min(r), max(r)
Check(atoms2).Update()
ReportTest.Summary()
for j in range(N):
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))
# Now the atoms are created from the positions and a sufficiently
# large unit cell. The unit cell is uncritical as there are no
# periodic boundaries, and the atoms are able to move outside the unit
# cell, so in principle it should work with the default
# 1-Angstrom-cube unit cell.
atoms = ListOfAtoms(positions=positions, cell=[max(positions[:,0]),
max(positions[:,1]),
max(positions[:,2])])
atoms.SetAtomicNumbers(element)
# Now the standard EMT Calculator is attached
atoms.SetCalculator(EMT())
# Make an object doing Langevin dynamics at a temperature of 800 K
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))