def update_qm_region_H(atoms):
"""
Set quantum region around the Hydrogen. Also records crackpos.
"""
mm_pot = Potential(mm_init_args,
param_filename = param_file,
cutoff_skin = cutoff_skin)
crack_pos = find_crack_tip_stress_field(atoms, calc=mm_pot)
#set quantum region to first hydrogen atom in list.
h_pos = atoms[h_list[0]].position
old_qm_list = atoms.hybrid_vec.nonzero()[0]
new_qm_list = update_hysteretic_qm_region(atoms, old_qm_list, h_pos,
qm_inner_radius,
qm_outer_radius,
update_marks=False)
#lets try setting the atoms object properties by hand?
atoms.hybrid[:] = 0
atoms.hybrid[new_qm_list] = 1
#Distributed Force Mixing Properties:
atoms.hybrid_vec[:] = 0
atoms.hybrid_vec[new_qm_list] = 1
atoms.hybrid_1[:] = atoms.hybrid_vec[:]
atoms.params['core'] = h_pos
atoms.params['CrackPos'] = crack_pos
return
def update_qm_region(atoms):
crack_pos = find_crack_tip_stress_field(atoms,
calc=mm_pot,
avg_sigma=avg_sigma)
qm_list = qmmm_pot.get_qm_atoms(atoms)
qm_list = update_hysteretic_qm_region(atoms, qm_list, crack_pos,
qm_inner_radius, qm_outer_radius)
qmmm_pot.set_qm_atoms(qm_list, atoms)
def update_qm_region(atoms=dynamics.atoms):
#crack_pos = find_crack_tip_stress_field(atoms, calc=mm_pot, avg_sigma=avg_sigma)
#print crack_pos
crack_pos = atoms.info['CrackPos']
qm_list = qmmm_pot.get_qm_atoms(atoms)
qm_list = update_hysteretic_qm_region(atoms, qm_list, crack_pos,
qm_inner_radius, qm_outer_radius)
qmmm_pot.set_qm_atoms(qm_list, 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
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
def update_qm_region(atoms, dis_type='edge', cut=3.0, rr=10.0, qr=1):
"""
Routine for updating qm region of dislocation.
Args:
dis_type: Dislocation type can be edge or screw.
rr: determines radius of quantum sphere.
qr: is the number of quantum regions.
"""
core[:] = atoms.params['core']
fixed_mask = (np.sqrt((atoms.positions[:,0]-core[0])**2 + (atoms.positions[:,1]-core[1])**2) < rr)
cl = atoms.select(mask=fixed_mask, orig_index=True)
print 'Number of Atoms in Cluster', cl.n
cl.set_cutoff(cut)
cl.calc_connect()
cl = Atoms(cl)
x0 = Atoms('ref_slab.xyz')
x0.set_cutoff(cut)
x0.calc_connect()
alpha = calc_nye_tensor(cl, x0, 3, 3, cl.n)
cl.screw = alpha[2,2,:]
cl.edge = alpha[2,0,:]
if dis_type == 'screw':
defect_pos = cl.screw
elif dis_type == 'edge':
defect_pos = cl.edge
total_def = 0.0
c = np.array([0.,0.,0.])
mom = [3.0 for at in range(len(atoms))]
atoms.set_initial_magnetic_moments(mom)
for i in range(cl.n):
defect_pos = defect_pos + cl.edge[i]
c[1] = c[1] + cl.positions[i,0]*defect_pos[i]
c[2] = c[2] + cl.pos[i,0]*defect_pos[i]
c[0] = c[0]/total_def
c[1] = c[1]/total_def
c[2] = atoms.lattice[2,2]/2.
core[:] = c.copy()
old_qm_list = atoms.hybrid_vec.nonzero()[0]
new_qm_list = update_hysteretic_qm_region(atoms, old_qm_list, core[:],
qm_inner_radius,
qm_outer_radius,
update_marks=False)
#Force Mixing Potential requires hybrid property:
atoms.hybrid[:] = 0
atoms.hybrid[new_qm_list] = 1
#Distributed Force Mixing Properties:
atoms.hybrid_vec[:] = 0
atoms.hybrid_vec[new_qm_list] = 1
atoms.hybrid_1[:] = atoms.hybrid_vec[:]
atoms.params['core'] = core[:]
return
def update_qm_region_crack(atoms):
mm_pot = Potential(params.mm_init_args,
param_filename=params.param_file,
cutoff_skin=params.cutoff_skin)
crack_pos = find_crack_tip_stress_field(atoms, calc=mm_pot)
old_qm_list = atoms.hybrid_vec.nonzero()[0]
new_qm_list = update_hysteretic_qm_region(atoms, old_qm_list, crack_pos,
params.qm_inner_radius,
params.qm_outer_radius,
update_marks=False)
#lets try setting the atoms object properties by hand?
atoms.hybrid[:] = 0
atoms.hybrid[new_qm_list] = 1
#Distributed Force Mixing Properties:
atoms.hybrid_vec[:] = 0
atoms.hybrid_vec[new_qm_list] = 1
atoms.hybrid_1[:] = atoms.hybrid_vec[:]
atoms.params['core'] = crack_pos
atoms.params['CrackPos'] = crack_pos
return
def update_qm_region(atoms):
crack_pos = find_crack_tip_stress_field(atoms, calc=mm_pot, avg_sigma=avg_sigma)
qm_list = qmmm_pot.get_qm_atoms(atoms)
qm_list = update_hysteretic_qm_region(atoms, qm_list, crack_pos,
qm_inner_radius, qm_outer_radius)
qmmm_pot.set_qm_atoms(qm_list, atoms)
lotf_spring_hops=3,
terminate=False,
calc_connect=True,
buffer_hops=3,
hysteretic_buffer=True,
cluster_vacuum = 5.0,
cluster_hopping = True,
single_cluster=True,
hysteretic_buffer_inner_radius=qm_inner_radius,
hysteretic_buffer_outer_radius=qm_outer_radius,
cluster_hopping_nneighb_only=True,
min_images_only=True)
atoms.set_calculator(qmmm_pot)
qmmm_pot.atoms = atoms
qm_list = update_hysteretic_qm_region(atoms, [], crack_pos, qm_inner_radius, qm_outer_radius)
atoms.hybrid[qm_list] = HYBRID_ACTIVE_MARK
dynamics = LOTFDynamics(atoms, timestep, extrapolate_steps, check_force_error=args.check_force)
if args.check_force:
pred_corr_logfile = open('pred-corr-error.txt','w')
dynamics.attach(log_pred_corr_errors, 1, dynamics, pred_corr_logfile)
# array to store time averaged stress field
avg_sigma = np.zeros((len(atoms), 3, 3))
def update_qm_region(atoms):
crack_pos = find_crack_tip_stress_field(atoms, calc=mm_pot, avg_sigma=avg_sigma)
qm_list = qmmm_pot.get_qm_atoms(atoms)
qm_list = update_hysteretic_qm_region(atoms, qm_list, crack_pos,
qm_inner_radius, qm_outer_radius)
qmmm_pot.set_qm_atoms(qm_list, atoms)
'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,
fit_hops=4,
lotf_spring_hops=3,
buffer_hops=4)
# Use the force mixing potential as the Atoms' calculator
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)
# *** Milestone 3.1 -- exit early - we don't want to run the classical MD! ***
import sys
sys.exit(0)
# **** no changes compared to run_crack_classical.py below here yet ****
# ********* 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)
if not params.continuation and not params.classical:
print 'Finding initial Quantum Core positions...'
if geom =='disloc':
atoms = set_quantum_disloc(atoms)
elif geom=='crack':
mom = [3.0 for at in range(len(atoms))]
atoms.set_initial_magnetic_moments(mom)
atoms.add_property('hybrid', 0, overwrite=True)
atoms.add_property('hybrid_vec', 0, overwrite=True)
atoms.add_property('hybrid_1', 0)
atoms.add_property('hybrid_mark_1', 0)
crackpos = atoms.info['CrackPos']
qm_list_old = []
qm_list = update_hysteretic_qm_region(atoms, [], crackpos, params.qm_inner_radius,
params.qm_outer_radius,
update_marks=False)
atoms.hybrid[qm_list] = HYBRID_ACTIVE_MARK
atoms.hybrid_vec[qm_list] = HYBRID_ACTIVE_MARK
atoms.hybrid_1[qm_list] = HYBRID_ACTIVE_MARK
atoms.hybrid_mark_1[qm_list] = HYBRID_ACTIVE_MARK
atoms.params['core'] = crackpos
print HYBRID_ACTIVE_MARK
print 'Core Found. No. Quantum Atoms:', sum(atoms.hybrid[:])
else:
print 'No cell geometry given, specifiy either disloc or crack', 1/0
# ********* Setup and run MD ***********
# Set the initial temperature to 2*simT: it will then equilibriate to
# simT, by the virial theorem
if params.test_mode:
