print("sputter event detected, equilibration...")
displacement = True
sputteringevents[0, nosputt] = nel
# electron number
sputteringevents[1, nosputt] = theta
# scattering angle chosen
sputteringevents[2, nosputt] = E_t
# transferred Energy to atom
sputteringevents[3, nosputt] = atomid
# atom chosen for energy transfer
#sputteringevents[4,nosputt] = partdisp; # atom lost
#sputteringevents[5,nosputt] = 1; # element1
nosputt += 1
# reset LAMMPS:
L.clear()
#L.close()
lmp = lammps()
L = PyLammps(ptr=lmp)
L.read_restart("restartfromprevdispl.equil")
L.pair_style("hybrid", "eam/alloy", "lj/cut", 10.0, "tersoff")
L.pair_coeff("* * eam/alloy NiAu_Zhou.eam.alloy Au Ni NULL")
L.pair_coeff(1, 3, "lj/cut", epsAuC, sigAuC, 10.0)
L.pair_coeff(2, 3, "lj/cut", epsNiC, sigNiC, 10.0)
L.pair_coeff("* *", "tersoff", "SiC.tersoff", "NULL NULL C")
L.compute("K", "all", "ke/atom")
L.compute("P", "all", "pe/atom")
L.compute(
"coordno", "all", "coord/atom", "cutoff", NNthresh
def test_use_data_file(self):
L = PyLammps()
L.units('real') # angstrom, kcal/mol, femtoseconds
L.atom_style('atomic')
L.boundary('p p p')
L.lattice('none', 1.0)
# create simulation cell
L.region('r1 block', -15.0, 15.0, -15.0, 15.0, -15.0, 15.0)
L.create_box(1, 'r1')
# argon
L.mass(1, 39.948002)
L.pair_style('lj/cut', 8.5)
L.pair_coeff(1, 1, 0.2379, 3.405)
L.timestep(10.0)
L.create_atoms(1, 'single', -1.0, 0.0, 0.0)
L.create_atoms(1, 'single', 1.0, 0.0, 0.0)
L.velocity('all create', 250.0, 54321, 'mom no rot no')
L.minimize(1.0e-10, 1.0e-10, 100, 1000)
L.reset_timestep(0)
L.thermo(100)
L.fix('f1 all nve')
L.run(1000)
L.write_restart('run.restart')
L.write_data('run.data')
L2 = PyLammps()
L2.units('real') # angstrom, kcal/mol, femtoseconds
L2.atom_style('atomic')
L2.boundary('p p p')
L2.pair_style('lj/cut', 8.5)
L2.read_data('run.data')
L2.timestep(10.0)
L2.thermo(100)
L2.fix('f1 all nve')
L2.run(1000)
# reset status. forget all settings. delete system
L2.clear()
L2.read_restart('run.restart')
L2.thermo(100)
L2.fix('f1 all nve')
L2.run(1000)
os.remove('run.restart')
os.remove('run.data')
self.assertEqual(L.system, L2.system)