# Increase epsilon_yy applied to all atoms at constant strain rate
strain_atoms = ConstantStrainRate(orig_height, strain_rate*timestep)
atoms.set_constraint([fix_atoms, strain_atoms])
# ******* Set up potentials and calculators ********
mm_pot = Potential(mm_init_args,
param_filename=param_file,
cutoff_skin=cutoff_skin)
# Request Potential to compute per-atom stresses whenever we
# compute forces, to save time when locating the crack tip
mm_pot.set_default_quantities(['stresses'])
# Density functional tight binding (DFTB) potential
qm_pot = Potential(qm_init_args,
param_filename=param_file)
# Parameters which control how the QM calculation is carried out:
# we use a single cluster, periodic in the z direction and terminated
# with hydrogen atoms. The positions of the outer layer of buffer atoms
# are not randomised.
qm_args_str = ('single_cluster cluster_periodic_z '+
'carve_cluster terminate randomise_buffer=F')
# Construct the QM/MM potential, which mixes QM and MM forces
qmmm_pot = ForceMixingPotential(pot1=mm_pot, pot2=qm_pot,
qm_args_str=qm_args_str,
# Increase epsilon_yy applied to all atoms at constant strain rate
strain_atoms = ConstantStrainRate(orig_height, strain_rate*timestep)
atoms.set_constraint([fix_atoms, strain_atoms])
# ******* Set up potentials and calculators ********
mm_pot = Potential(mm_init_args,
param_filename=param_file,
cutoff_skin=cutoff_skin)
# Request Potential to compute per-atom stresses whenever we
# compute forces, to save time when locating the crack tip
mm_pot.set_default_quantities(['stresses'])
atoms.set_calculator(mm_pot)
# ********* Setup and run MD ***********
# Set the initial temperature to 2*simT: it will then equilibriate to
# simT, by the virial theorem
MaxwellBoltzmannDistribution(atoms, 2.0*sim_T)
# Initialise the dynamical system
dynamics = VelocityVerlet(atoms, timestep)
# Print some information every time step
def printstatus():
if dynamics.nsteps == 1: