test examples for asap

test/examples/md.py

+from __future__ import print_function
+
+from ase.lattice.cubic import FaceCenteredCubic
+from ase.md.langevin import Langevin
+from ase.io.trajectory import Trajectory
+from ase import units
+
+#from asap3 import EMT  # Way too slow with ase.EMT !
+from ase.calculators.emt import EMT
+size = 2
+
+T = 1500  # Kelvin
+
+# Set up a crystal
+atoms = FaceCenteredCubic(directions=[[1, 0, 0], [0, 1, 0], [0, 0, 1]],
+                          symbol="Cu",
+                          size=(size, size, size),
+                          pbc=False)
+
+# Describe the interatomic interactions with the Effective Medium Theory
+atoms.set_calculator(EMT())
+
+# We want to run MD with constant energy using the Langevin algorithm
+# with a time step of 5 fs, the temperature T and the friction
+# coefficient to 0.02 atomic units.
+dyn = Langevin(atoms, 5 * units.fs, T * units.kB, 0.002)
+
+
+def printenergy(a=atoms):  # store a reference to atoms in the definition.
+    """Function to print the potential, kinetic and total energy."""
+    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))
+
+dyn.attach(printenergy, interval=50)
+
+# We also want to save the positions of all atoms after every 100th time step.
+traj = Trajectory('moldyn2.traj', 'w', atoms)
+dyn.attach(traj.write, interval=50)
+
+# Now run the dynamics
+printenergy()
+dyn.run(5000)