atoms.set_calculator(qmmm_pot)
# *** Set up the initial QM region ****
qm_list = update_hysteretic_qm_region(atoms, [], orig_crack_pos,
qm_inner_radius, qm_outer_radius)
qmmm_pot.set_qm_atoms(qm_list)
# ********* 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 = LOTFDynamics(atoms, timestep, extrapolate_steps)
# Print some information every time step
def printstatus():
if dynamics.nsteps == 1:
print """
State Time/fs Temp/K Strain G/(J/m^2) CrackPos/A D(CrackPos)/A
---------------------------------------------------------------------------------"""
log_format = (
'%(label)-4s%(time)12.1f%(temperature)12.6f' +
'%(strain)12.5f%(G)12.4f%(crack_pos_x)12.2f (%(d_crack_pos_x)+5.2f)'
)
atoms.info['label'] = dynamics.state_label # Label for the status line
try:
defect.params['core']
except KeyError:
defect.params['core'] = np.array([98.0, 98.0, 1.49])
defect = set_quantum(defect, params.n_core)
MaxwellBoltzmannDistribution(defect, 2.0 * sim_T)
if dyn_type == 'eam':
dynamics = VelocityVerlet(defect, timestep)
dynamics.attach(pass_print_context(defect, dynamics))
elif dyn_type == 'LOTF':
defect.info['core'] = np.array([98.0, 98.0, 1.49])
print 'Initializing LOTFDynamics'
verbosity_push(PRINT_VERBOSE)
dynamics = LOTFDynamics(defect,
timestep,
params.extrapolate_steps,
check_force_error=False)
dynamics.set_qm_update_func(update_qm_region)
dynamics.attach(pass_print_context(defect, dynamics))
dynamics.attach(traj_writer, print_interval, defect)
else:
print 'No dyn_type chosen', 1 / 0
trajectory = AtomsWriter('{0}.traj.xyz'.format(input_file))
print 'Running Crack Simulation'
dynamics.run(nsteps)
#Write cooked i.e. thermalized ceel to file.
defect.set_cutoff(3.0)
defect.calc_connect()
new_core = pp_nye_tensor(defect, dis_type=dis_type)
defect.info['core'] = new_core
# *** Set up the initial QM region ****
qm_list = update_hysteretic_qm_region(atoms, [], orig_crack_pos,
qm_inner_radius, qm_outer_radius)
qmmm_pot.set_qm_atoms(qm_list)
# ********* 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 = LOTFDynamics(atoms,
timestep,
extrapolate_steps,
check_force_error=True)
# Print some information every time step
def printstatus():
if dynamics.nsteps == 1:
print """
State Time/fs Temp/K Strain G/(J/m^2) CrackPos/A D(CrackPos)/A
---------------------------------------------------------------------------------"""
log_format = (
'%(label)-4s%(time)12.1f%(temperature)12.6f' +
'%(strain)12.5f%(G)12.4f%(crack_pos_x)12.2f (%(d_crack_pos_x)+5.2f)'
)
MaxwellBoltzmannDistribution(atoms, 2.0*sim_T)
# Save frames to the trajectory every `traj_interval` time steps
# but only when interpolating
trajectory = AtomsWriter(os.path.join(params.rundir, params.traj_file))
# Initialise the dynamical system
system_timer('init_dynamics')
if params.extrapolate_steps == 1:
dynamics = VelocityVerlet(atoms, params.timestep)
check_force_error = False
if not params.classical:
qmmm_pot.set(calc_weights=True)
dynamics.state_label = 'D'
else:
print 'Initializing LOTF Dynamics'
dynamics = LOTFDynamics(atoms, params.timestep,
params.extrapolate_steps,
check_force_error=check_force_error)
system_timer('init_dynamics')
#Function to update the QM region at the beginning of each extrapolation cycle
if not check_force_error:
if params.extrapolate_steps == 1:
if not params.classical:
dynamics.attach(update_qm_region, 1, dynamics.atoms)
else:
# choose appropriate update function for defects or crack.
# or grainboundary.
print 'Setting Update Function'
if geom =='disloc':
dynamics.set_qm_update_func(update_qm_region)
elif geom =='crack':
dynamics.set_qm_update_func(update_qm_region_crack)
print 'Running WITH EAM as embedded cluster'
qm_pot_file = os.path.join(pot_dir, 'PotBH_fakemod.xml')
print qm_pot_file
mm_init_args = 'IP EAM_ErcolAd do_rescale_r=T r_scale=1.01' # Classical potential
qm_pot = Potential(mm_init_args, param_filename=qm_pot_file, cutoff_skin=cutoff_skin)
qmmm_pot = set_qmmm_pot(atoms, atoms.params['CrackPos'], mm_pot, qm_pot)
strain_atoms = fix_edges(atoms)
print 'Setup dynamics'
#If input_file is crack.xyz the cell has not been thermalized yet.
#Otherwise it will recover temperature from the previous run.
print 'Attaching trajectories to dynamics'
trajectory = AtomsWriter(traj_file)
#Only wriates trajectory if the system is in the LOTFDynamicas
#Interpolation
atoms.wrap()
atoms.set_cutoff(3.0)
atoms.calc_connect()
print 'Running Crack Simulation'
RELAXATION = False
if RELAXATION:
dynamics = FIRE(atoms)
dynamics.attach(pass_trajectory_context(trajectory, dynamics), traj_interval, dynamics)
dynamics.run(fmax=0.1)
else:
dynamics = LOTFDynamics(atoms, timestep, extrapolate_steps)
dynamics.attach(pass_trajectory_context(trajectory, dynamics), traj_interval, dynamics)
nsteps = 2000
dynamics.run(nsteps)
pickle.dump(crack_dict,f)
# Save frames to the trajectory every `traj_interval` time steps.
trajectory = AtomsWriter(os.path.join(rundir, traj_file))
# Initialise the dynamical system
system_timer('init_dynamics')
if extrapolate_steps == 1:
dynamics = VelocityVerlet(atoms, timestep)
check_force_error = False
if not classical:
qmmm_pot.set(calc_weights=True)
dynamics.state_label = 'D'
else:
print 'Initializing LOTF Dynamics'
dynamics = LOTFDynamics(atoms, timestep,
extrapolate_steps,
check_force_error=check_force_error)
system_timer('init_dynamics')
# Function to update the QM region at the beginning of each extrapolation cycle
if not check_force_error:
if extrapolate_steps == 1:
if not classical:
dynamics.attach(update_qm_region, 1, dynamics.atoms)
else:
# Choose appropriate update function for defects or crack or grainboundary
print 'Setting Update Function'
if geom =='disloc':
dynamics.set_qm_update_func(update_qm_region)
elif geom =='crack':
if quantumregion == 'Crack':
dynamics.set_qm_update_func(update_qm_region_crack)
atoms.set_calculator(qmmm_pot)
del_keys = ['force', 'forces', 'forces0']
array_keys = atoms.arrays.keys()
prop_keys = atoms.properties.keys()
for key in del_keys:
if key in array_keys:
del (atoms.arrays[key])
#under construction
if False:
np.random.seed(42)
MaxwellBoltzmannDistribution(atoms, 2.0 * sim_T)
check_force_error = False
dynamics = LOTFDynamics(atoms,
timestep,
extrapolate_steps,
check_force_error=check_force_error)
def log_pred_corr_errors(dynamics, logfile):
logline = '%s err %10.1f%12.6f%12.6f\n' % (
dynamics.state_label, dynamics.get_time() / units.fs,
dynamics.rms_force_error, dynamics.max_force_error)
print logline
logfile.write(logline)
if check_force_error:
pred_corr_logfile = open('pred-corr-error.txt', 'w')
dynamics.attach(log_pred_corr_errors, 1, dynamics, pred_corr_logfile)
return check_if_cracked
def update_qm_region_context(qmmm_pot, mm_pot, atoms):
def update_qm_region(atoms):
crack_pos = find_crack_tip_stress_field(atoms, calc=mm_pot)
qm_list = qmmm_pot.get_qm_atoms()
qm_list = update_hysteretic_qm_region(atoms, qm_list, crack_pos, qm_inner_radius,
qm_outer_radius, update_marks=True)
qmmm_pot.set_qm_atoms(qm_list)
#lets try setting the atoms object properties by hand?
atoms.hybrid[:] = HYBRID_NO_MARK
atoms.hybrid[qm_list] = HYBRID_ACTIVE_MARK
return update_qm_region
if __name__=='__main__':
#Randomize initial positions
np.random.seed()
MaxwellBoltzmannDistribution(atoms, 2.0*sim_T)
#dynamics = VelocityVerlet(atoms, timestep)
dynamics = LOTFDynamics(atoms, timestep, extrapolate_steps)
dynamics.attach(check_if_cracked, 1, atoms)
dynamics = LOTFDynamics(atoms, timestep, extrapolate_steps)
dynamics.set_qm_update_func(update_qm_region)
#Writing the trajectory
trajectory = AtomsWriter(traj_file)
dynamics.attach(traj_writer, traj_interval, dynamics)
dynamics.attach(printstatus)
print 'Running Crack Simulation'
dynamics.run(nsteps)
print 'Crack Simulation Finished'