print 'Finding initial dislocation core positions...'
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()
def makecrack_main(params, stem):
"""Given a CrackParams object `param`, construct and return a new crack slab Atoms object."""
xmlfilename = stem+'.xml'
print_title('Initialisation')
verbosity_push(params.io_verbosity)
params.print_()
print("Initialising classical potential with args " + params.classical_args.strip() +
" from file " + xmlfilename)
classicalpot = Potential(params.classical_args, param_filename=xmlfilename)
classicalpot.print_()
mpi_glob = MPI_context()
crack_slab, width, height, E, v, v2, bulk = crack_make_slab(params, classicalpot)
if params.crack_free_surfaces:
depth = crack_slab.pos[3,:].max() - crack_slab.pos[3,:].min()
else:
depth = crack_slab.lattice[3,3]
# Save bulk cube (used for qm_rescale_r parameter in crack code)
if params.qm_args.startswith('TB'):
bigger_bulk = supercell(bulk, 2, 2, 2)
bulk = bigger_bulk
bulk.write(stem+'_bulk.xyz')
crack_slab.write(stem+'_slab.xyz')
crack_slab.params['OrigWidth'] = width
crack_slab.params['OrigHeight'] = height
crack_slab.params['OrigDepth'] = depth
crack_slab.params['YoungsModulus'] = E
crack_slab.params['PoissonRatio_yx'] = v
crack_slab.params['PoissonRatio_yz'] = v2
# Open surfaces, remain periodic in z direction (normal to plane)
# and optionally also in x direction if crack_double_ended is true
if not params.crack_double_ended:
crack_slab.lattice[1,1] = crack_slab.lattice[1,1] + params.crack_vacuum_size
crack_slab.lattice[2,2] = crack_slab.lattice[2,2] + params.crack_vacuum_size
crack_slab.set_lattice(crack_slab.lattice, False)
# 3D crack with free surfaces at z = +/- depth/2
if params.crack_free_surfaces:
crack_slab.pos[3,:] -= crack_slab.pos[3,:].mean() # center on z=0
crack_slab.lattice[3,3] = crack_slab.lattice[3,3] + params.crack_vacuum_size
crack_slab.set_lattice(crack_slab.lattice, False)
# Map atoms into cell AFTER changing to the new lattice
crack_slab.map_into_cell()
miny, maxy = crack_slab.pos[2,:].min(), crack_slab.pos[2,:].max()
assert abs((maxy-miny) - height) < 1e-5 # be sure that remapping didn't change height of slab
# Add various properties to crack_slab
crack_slab.add_property('hybrid', 0)
crack_slab.add_property('hybrid_mark', HYBRID_NO_MARK)
crack_slab.add_property('changed_nn', 0)
crack_slab.add_property('move_mask', 0)
crack_slab.add_property('nn', 0)
crack_slab.add_property('old_nn', 0)
crack_slab.add_property('md_old_changed_nn', 0)
crack_slab.add_property('edge_mask', 0)
crack_slab.add_property('crack_surface', False)
crack_slab.add_property('crack_front', False)
if params.crack_fix_dipoles:
crack_slab.add_property('fixdip', False)
print_title('Fixing Atoms')
# Fix top and bottom edges - anything within crack_edge_fix_tol of ymax or ymin is fixed
miny, maxy = crack_slab.pos[2,:].min(), crack_slab.pos[2,:].max()
crack_slab.move_mask[:] = 1
crack_slab.move_mask[(abs(crack_slab.pos[2,:]-maxy) < params.crack_edge_fix_tol) |
(abs(crack_slab.pos[2,:]-miny) < params.crack_edge_fix_tol)] = 0
if params.crack_fix_sides:
maxx, minx = crack_slab.pos[1,:].min(), crack_slab.pos[1,:].max()
crack_slab.move_mask[(abs(crack_slab.pos[1,:]-maxx) < params.crack_edge_fix_tol) |
(abs(crack_slab.pos[1,:]-minx) < params.crack_edge_fix_tol)] = 0
print('%d atoms. %d fixed atoms' % (crack_slab.n, crack_slab.n - crack_slab.move_mask.sum()))
print_title('Setting edge mask')
crack_slab.edge_mask[:] = 0
minx, maxx = crack_slab.pos[1,:].min(), crack_slab.pos[1,:].max()
crack_slab.edge_mask[(abs(crack_slab.pos[1,:]-minx) < params.selection_edge_tol) |
(abs(crack_slab.pos[1,:]-maxx) < params.selection_edge_tol)] = 1
miny, maxy = crack_slab.pos[2,:].min(), crack_slab.pos[2,:].max()
crack_slab.edge_mask[(abs(crack_slab.pos[2,:]-miny) < params.selection_edge_tol) |
(abs(crack_slab.pos[2,:]-maxy) < params.selection_edge_tol)] = 1
if params.crack_free_surfaces:
# Open surfaces at +/- z
minz, maxz = crack_slab.pos[3,:].min(), crack_slab.pos[3,:].max()
crack_slab.edge_mask[(abs(crack_slab.pos[3,:]-minz) < params.selection_edge_tol) |
(abs(crack_slab.pos[3,:]-maxz) < params.selection_edge_tol)] = 1
if params.crack_fix_dipoles:
print_title('Fixing dipoles')
crack_slab.fixdip[(abs(crack_slab.pos[2,:]-maxy) < params.crack_fix_dipoles_tol) |
(abs(crack_slab.pos[2,:]-miny) < params.crack_fix_dipoles_tol)] = 1
if params.crack_fix_sides:
maxx, minx = crack_slab.pos[1,:].min(), crack_slab.pos[1,:].max()
crack_slab.fixdip[(abs(crack_slab.pos[1,:]-maxx) < params.crack_fix_dipoles_tol) |
(abs(crack_slab.pos[1,:]-minx) < params.crack_fix_dipoles_tol)] = 1
if params.crack_curved_front:
crack_make_seed_curved_front(crack_slab, params)
else:
crack_make_seed(crack_slab, params)
if params.crack_apply_initial_load:
crack_calc_load_field(crack_slab, params, classicalpot,
params.crack_loading, overwrite_pos=True,
mpi=mpi_glob)
crack_slab.write('dump.xyz')
crack_update_connect(crack_slab, params)
if not params.simulation_classical:
if (params.selection_method.strip() == 'crack_front' or
params.crack_tip_method.strip() == 'local_energy'):
classicalpot.calc(crack_slab, local_energy=True)
crack_setup_marks(crack_slab, params)
crack_update_selection(crack_slab, params)
if params.any_per_atom_tau():
# Set up per_atom_tau property for ramped Langevin thermostat:
#
# tau
# ^
# |\ /| |\ /| max_tau
# | \ / | | \ / |
# | \ / | constant E | \ / |
# | \ / | (tau = 0) | \ / |
# | \/ | | \/ |
# +----------+---------------------+----------+---> x
# -w/2 -w/2+r w/2-r w/2
w_by_2 = crack_slab.OrigWidth/2.
ramp_len = params.crack_thermostat_ramp_length
max_tau = params.crack_thermostat_ramp_max_tau
print 'Adding thermostat ramp with length', ramp_len, 'max_tau', max_tau
@np.vectorize
def tau(x):
if x < -w_by_2 + ramp_len/2:
q = (x+w_by_2)/(ramp_len/2.)
return max_tau*(1.- q)
elif (x > -w_by_2 + ramp_len/2 and
x < -w_by_2 + ramp_len):
q = (x+w_by_2-ramp_len/2.)/(ramp_len/2.)
return max_tau*q
elif (x > -w_by_2 + ramp_len and
x < w_by_2 - ramp_len):
return 0.
elif (x > w_by_2 - ramp_len and
x < w_by_2 - ramp_len/2):
q = (x-w_by_2+ramp_len)/(ramp_len/2.)
return max_tau*(1.- q)
else:
q = (x-w_by_2+ramp_len/2.)/(ramp_len/2.)
return max_tau*q
crack_slab.add_property('per_atom_tau', tau(crack_slab.pos[1,:]))
return crack_slab
print 'Finding initial dislocation core positions...'
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)