def __run_rand_dyn__(self, mid, T1, T2, dt, Nc, Ns, dS):
# Setup calculator
mol = self.mols[0].copy()
# Setup PBC if active
if self.pbc:
mol.set_cell(([[self.pbl, 0, 0],
[0, self.pbl, 0],
[0, 0, self.pbl]]))
mol.set_pbc((self.pbc, self.pbc, self.pbc))
# Setup calculator
mol.set_calculator(ANIENS(self.aens))
#mol.set_calculator(ANI(False))
#mol.calc.setnc(self.ncl[0])
# Set chemical symbols
spc = mol.get_chemical_symbols()
# Set the velocities corresponding to a boltzmann dist @ T/4.0
MaxwellBoltzmannDistribution(mol, T1 * units.kB)
# Set the thermostat
dyn = Langevin(mol, dt * units.fs, T1 * units.kB, 0.02)
dT = (T2 - T1)/Nc
#print('Running...')
for i in range(Nc):
# Set steps temperature
dyn.set_temperature((T1 + dT*i) * units.kB)
# Do Ns steps of dynamics
dyn.run(Ns)
# Return sigma
sigma = hdt.evtokcal * mol.calc.stddev
ekin = mol.get_kinetic_energy() / len(mol)
# Check for dynamics failure
if sigma > dS:
self.Nbad += 1
self.X.append(mol.get_positions())
#print('Step:', dyn.get_number_of_steps(), 'Sig:', sigma, 'Temp:',
# str(ekin / (1.5 * units.kB)) + '(' + str(T1 + dT * i) + ')')
return True,dyn.get_number_of_steps()
return False,dyn.get_number_of_steps()
results=crack_pos)
# run for 2000 time steps to reach steady state at initial load
for i in range(20):
dyn.run(100)
if extend_strip(dyn.atoms, params.a, params.N, params.M, params.vacuum):
set_constraints(dyn.atoms, params.a)
# start decreasing strain
#set_constraints(dyn.atoms, params.a, delta_strain=delta_strain)
strain_atoms = ConstantStrainRate(dyn.atoms.info['OrigHeight'], delta_strain)
dyn.attach(strain_atoms.apply_strain, 1, dyn.atoms)
for i in range(50):
dyn.run(100)
if extend_strip(dyn.atoms, params.a, params.N, params.M, params.vacuum):
set_constraints(dyn.atoms, params.a)
del dyn.observers[-1] # stop increasing the strain
for i in range(1000):
dyn.run(100)
if extend_strip(dyn.atoms, params.a, params.N, params.M, params.vacuum):
set_constraints(dyn.atoms, params.a)
traj.close()
time = 10.0 * dyn.dt * np.arange(dyn.get_number_of_steps() / 10)
np.savetxt('crackpos.dat', np.c_[time, crack_pos])
