def build_crack_cell(self, unit_slab, pot, fix_dist=1.0):
"""
Creates a CrackCell of the desired size and orientation
with the top and bottom layer of atoms constrained.
Returns: :class:`Atoms` - the relaxed crack_cell.
"""
self.nx = int(self.width/unit_slab.get_cell()[0,0])
self.ny = int(self.height/unit_slab.get_cell()[1,1])
if self.ny %2 == 1:
self.ny +=1
#self.ny = 1
print 'number of unit cells', self.nx, self.ny
crack_slab = unit_slab*(self.nx, self.ny,self.nz)
write('ref_slab.xyz', crack_slab)
crack_slab.center(self.vacuum, axis=0)
crack_slab.center(self.vacuum, axis=1)
crack_slab.positions[:, 0] -= crack_slab.positions[:, 0].mean()
crack_slab.positions[:, 1] -= crack_slab.positions[:, 1].mean()
self.orig_width = (crack_slab.positions[:, 0].max() -
crack_slab.positions[:, 0].min())
self.orig_height = (crack_slab.positions[:, 1].max() -
crack_slab.positions[:, 1].min())
print(('Made slab with %d atoms, original width and height: %.1f x %.1f A^2' %
(len(crack_slab), self.orig_width, self.orig_height)))
top = crack_slab.positions[:,1].max()
bottom = crack_slab.positions[:,1].min()
left = crack_slab.positions[:,0].min()
right = crack_slab.positions[:,0].max()
#Constrain top and bottom layer of atoms:
fixed_mask = ((abs(crack_slab.positions[:, 1] - top) < 1.0) |
(abs(crack_slab.positions[:, 1] - bottom) < 1.0))
const = FixAtoms(mask=fixed_mask)
crack_slab.set_constraint(const)
#Strain is a dimensionless ratio we require elastic tensor
#to translate the initial energy flow to the tip into a strain.
self.E = youngs_modulus(self.cij, self.cleavage_plane)
self.nu = poisson_ratio(self.cij, self.cleavage_plane, self.crack_direction)
self.strain = G_to_strain(self.initial_G, self.E, self.nu, self.orig_height)
seed = left + self.crack_seed_length
tip = left + self.crack_seed_length + self.strain_ramp_length
xpos = crack_slab.positions[:,0]
ypos = crack_slab.positions[:,1]
crack_slab.positions[:,1] += thin_strip_displacement_y(xpos, ypos, self.strain, seed, tip)
write('crack_slab_init.xyz', crack_slab)
print('Applied initial load: strain=%.4f, G=%.2f J/m^2' %
(self.strain, self.initial_G / (units.J / units.m**2)))
pot_dir = os.environ['POTDIR']
crack_slab.set_calculator(pot)
#Initial crack pos
print 'crack_pos before relaxations'
print find_crack_tip_stress_field(crack_slab, calc=mm_pot)
print('Relaxing slab...')
slab_opt = PreconFIRE(crack_slab)
slab_opt.run(fmax=self.relax_fmax)
return crack_slab
def check_if_cracked(atoms):
orig_crack_pos = atoms.info['CrackPos'].copy()
crack_pos = find_crack_tip_stress_field(atoms, calc=mm_pot)
if not atoms.info['is_cracked'] and (crack_pos[0] -
orig_crack_pos[0]) > tip_move_tol:
atoms.info['is_cracked'] = True
del atoms.constraints[atoms.constraints.index(strain_atoms)]
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 printstatus():
if (dynamics.nsteps % 10) == 0:
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)'
)
log_format2 = ('%(label)-4s%(time)12.1f%(temperature)12.6f')
try:
atoms.info[
'label'] = dynamics.state_label # Label for the status line
except AttributeError:
atoms.info['label'] = 'classical' # Label for the status line
atoms.info['time'] = dynamics.get_time() / units.fs
atoms.info['temperature'] = (atoms.get_kinetic_energy() /
(1.5 * units.kB * len(atoms)))
atoms.info['strain'] = get_strain(atoms)
try:
atoms.info['G'] = get_energy_release_rate(atoms) / (units.J /
units.m**2)
except:
atoms.info['G'] = 0.0
try:
orig_crack_pos = atoms.info['CrackPos'].copy()
crack_pos = find_crack_tip_stress_field(atoms, calc=mm_pot)
atoms.info['crack_pos_x'] = crack_pos[0]
atoms.info['d_crack_pos_x'] = crack_pos[0] - orig_crack_pos[0]
print log_format % atoms.info
except KeyError:
print log_format2 % atoms.info
def printstatus():
if (dynamics.nsteps%10)==0:
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)')
log_format2 = ('%(label)-4s%(time)12.1f%(temperature)12.6f')
try:
atoms.info['label'] = dynamics.state_label # Label for the status line
except AttributeError:
atoms.info['label'] = 'classical' # Label for the status line
atoms.info['time'] = dynamics.get_time()/units.fs
atoms.info['temperature'] = (atoms.get_kinetic_energy() /
(1.5*units.kB*len(atoms)))
atoms.info['strain'] = get_strain(atoms)
try:
atoms.info['G'] = get_energy_release_rate(atoms)/(units.J/units.m**2)
except:
atoms.info['G'] = 0.0
try:
orig_crack_pos = atoms.info['CrackPos'].copy()
crack_pos = find_crack_tip_stress_field(atoms, calc=mm_pot)
atoms.info['crack_pos_x'] = crack_pos[0]
atoms.info['d_crack_pos_x'] = crack_pos[0] - orig_crack_pos[0]
print log_format % atoms.info
except KeyError:
print log_format2 % atoms.info
def check_if_cracked(atoms):
crack_pos = find_crack_tip_stress_field(atoms, calc=mm_pot)
# stop straining if crack has advanced more than tip_move_tol
if not atoms.info['is_cracked'] and (crack_pos[0] - orig_crack_pos[0]) > tip_move_tol:
atoms.info['is_cracked'] = True
del atoms.constraints[atoms.constraints.index(strain_atoms)]
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
atoms.info['time'] = dynamics.get_time() / units.fs
atoms.info['temperature'] = (atoms.get_kinetic_energy() /
(1.5 * units.kB * len(atoms)))
atoms.info['strain'] = get_strain(atoms)
atoms.info['G'] = get_energy_release_rate(atoms) / (units.J / units.m**2)
crack_pos = find_crack_tip_stress_field(atoms,
calc=mm_pot,
avg_sigma=avg_sigma)
atoms.info['crack_pos_x'] = crack_pos[0]
atoms.info['d_crack_pos_x'] = crack_pos[0] - orig_crack_pos[0]
print log_format % atoms.info
def check_if_cracked(atoms):
crack_pos = find_crack_tip_stress_field(atoms, calc=mm_pot)
# stop straining if crack has advanced more than tip_move_tol
if not atoms.info['is_cracked'] and (crack_pos[0] - orig_crack_pos[0]) > tip_move_tol:
atoms.info['is_cracked'] = True
del atoms.constraints[atoms.constraints.index(strain_atoms)]
def atom_straining(atoms):
crack_pos = find_crack_tip_stress_field(atoms, calc=mm_pot)
# keep straining until the crack tip has advanced to tip_move_tol
if not atoms.info['is_cracked'] and (crack_pos[0] -
orig_crack_pos[0]) < tip_move_tol:
strain_atoms.apply_strain(atoms)
elif not atoms.info['is_cracked']:
atoms.info['is_cracked'] = True
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):
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_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 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'] = 'D' # Label for the status line
atoms.info['time'] = dynamics.get_time()/units.fs
atoms.info['temperature'] = (atoms.get_kinetic_energy() /
(1.5*units.kB*len(atoms)))
atoms.info['strain'] = get_strain(atoms)
atoms.info['G'] = get_energy_release_rate(atoms)/(units.J/units.m**2)
crack_pos = find_crack_tip_stress_field(atoms, calc=mm_pot)
atoms.info['crack_pos_x'] = crack_pos[0]
atoms.info['d_crack_pos_x'] = crack_pos[0] - orig_crack_pos[0]
print log_format % atoms.info
def write_crack_cell(self, crack_slab, mm_pot):
print crack_slab.get_cell()
crack_slab.info['nneightol'] = 1.30 # set nearest neighbour tolerance
crack_slab.info['LatticeConstant'] = self.a0
crack_slab.info['C11'] = self.cij[0, 0]
crack_slab.info['C12'] = self.cij[0, 1]
crack_slab.info['C44'] = self.cij[3, 3]
crack_slab.info['YoungsModulus'] = self.E
crack_slab.info['PoissonRatio_yx'] = self.nu
crack_slab.info['G'] = self.initial_G
crack_slab.info['OrigWidth'] = self.orig_width
crack_slab.info['OrigHeight'] = self.orig_height
crack_slab.info['CrackDirection'] = self.crack_direction
crack_slab.info['CleavagePlane'] = self.cleavage_plane
crack_slab.info['CrackFront'] = self.crack_front
crack_slab.info['strain'] = self.strain
#Initial guess for crack_pos
crack_slab.info['CrackPos'] = np.array([1.5, 1.5, 1.5])
crack_pos = find_crack_tip_stress_field(crack_slab, calc=mm_pot)
print 'Found crack tip at position %s' % crack_pos
crack_slab.info['CrackPos'] = crack_pos
crack_slab.info['is_cracked'] = False
write('crack.xyz', crack_slab)
def write_crack_cell(self, crack_slab, mm_pot):
print crack_slab.get_cell()
crack_slab.info['nneightol'] = 1.30 # set nearest neighbour tolerance
crack_slab.info['LatticeConstant'] = self.a0
crack_slab.info['C11'] = self.cij[0, 0]
crack_slab.info['C12'] = self.cij[0, 1]
crack_slab.info['C44'] = self.cij[3, 3]
crack_slab.info['YoungsModulus'] = self.E
crack_slab.info['PoissonRatio_yx'] = self.nu
crack_slab.info['G'] = self.initial_G
crack_slab.info['OrigWidth'] = self.orig_width
crack_slab.info['OrigHeight'] = self.orig_height
crack_slab.info['CrackDirection'] = self.crack_direction
crack_slab.info['CleavagePlane'] = self.cleavage_plane
crack_slab.info['CrackFront'] = self.crack_front
crack_slab.info['strain'] = self.strain
#Initial guess for crack_pos
crack_slab.info['CrackPos'] = np.array([1.5, 1.5, 1.5])
crack_pos = find_crack_tip_stress_field(crack_slab, calc=mm_pot)
print 'Found crack tip at position %s' % crack_pos
crack_slab.info['CrackPos'] = crack_pos
crack_slab.info['is_cracked'] = False
write('crack.xyz', crack_slab)
def check_if_cracked(atoms):
orig_crack_pos = atoms.info['CrackPos'].copy()
crack_pos = find_crack_tip_stress_field(atoms, calc=mm_pot)
if not atoms.info['is_cracked'] and (crack_pos[0] - orig_crack_pos[0]) > tip_move_tol:
atoms.info['is_cracked'] = True
del atoms.constraints[atoms.constraints.index(strain_atoms)]
crack_slab.positions[:, 0],
crack_slab.positions[:, 1],
strain,
left + crack_seed_length,
left + crack_seed_length + strain_ramp_length)
print('Applied initial load: strain=%.4f, G=%.2f J/m^2' %
(strain, initial_G / (units.J / units.m**2)))
crack_slab.set_calculator(mm_pot)
minim = Minim(crack_slab, relax_positions=True, relax_cell=False)
minim.run(fmax=relax_fmax)
# Find initial position of crack tip
crack_pos = find_crack_tip_stress_field(crack_slab, calc=mm_pot)
print 'Found crack tip at position %s' % crack_pos
# Save all calculated materials properties inside the Atoms object
crack_slab.info['nneightol'] = 1.3 # nearest neighbour tolerance
crack_slab.info['LatticeConstant'] = 5.431
crack_slab.info['C11'] = c[0, 0]
crack_slab.info['C12'] = c[0, 1]
crack_slab.info['C44'] = c[3, 3]
crack_slab.info['YoungsModulus'] = E
crack_slab.info['PoissonRatio_yx'] = nu
crack_slab.info['SurfaceEnergy'] = gamma
crack_slab.info['OrigWidth'] = orig_width
crack_slab.info['OrigHeight'] = orig_height
crack_slab.info['CrackDirection'] = crack_direction
crack_slab.info['CleavagePlane'] = cleavage_plane
crack_slab.positions[:, 0], crack_slab.positions[:, 1], strain,
left + crack_seed_length, left + crack_seed_length + strain_ramp_length)
print('Applied initial load: strain=%.4f, G=%.2f J/m^2' %
(strain, initial_G / (units.J / units.m**2)))
# ***** Relaxation of crack slab *****
# optionally, relax the slab, keeping top and bottom rows fixed
print('Relaxing slab...')
crack_slab.set_calculator(mm_pot)
minim = Minim(crack_slab, relax_positions=True, relax_cell=False)
minim.run(fmax=0.01)
# Find initial position of crack tip
crack_pos = find_crack_tip_stress_field(crack_slab, calc=mm_pot)
crack_pos = find_crack_tip_coordination(crack_slab,
edge_tol=10.0,
strip_height=30.0,
nneightol=1.3)
print 'Found crack tip at position %s' % crack_pos
# Save all calculated materials properties inside the Atoms object
crack_slab.info['CrackPos'] = crack_pos
crack_slab.info['is_cracked'] = False
# ******** Save output file **********
# save results in extended XYZ format, including extra properties and info
print('Writing crack slab to file %s' % output_file)
pred_corr_logfile.close()
else:
mm_pot = Potential(mm_init_args, param_filename=pot_file, cutoff_skin=cutoff_skin)
atoms = AtomsReader(args.input_file)[-1]
atoms.set_calculator(mm_pot)
if args.restart:
#delete certain keys so they don't cause problem in write_xyz.
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])
strain_atoms = fix_edges(atoms)
current_crack_pos = find_crack_tip_stress_field(atoms, calc=mm_pot)
print 'Current Crack Position: ', current_crack_pos
if not args.restart:
print 'Thermalizing Atoms'
MaxwellBoltzmannDistribution(atoms, 2.0*sim_T)
dynamics = VelocityVerlet(atoms, timestep)
def print_context(ats=atoms, dyn=dynamics):
print 'steps, T', dyn.nsteps, ats.get_kinetic_energy()/(1.5*units.kB*len(ats))
print 'G', get_energy_release_rate(ats)/(units.J/units.m**2)
print 'strain', get_strain(ats)
#for 0.25 fs time step we have an image every half
#phonon cycle which is plenty
dynamics.attach(print_context, interval=32)
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 build_crack_cell(self, unit_slab, pot, fix_dist=1.0):
"""
Creates a CrackCell of the desired size and orientation
with the top and bottom layer of atoms constrained.
Returns: :class:`Atoms` - the relaxed crack_cell.
"""
self.nx = int(self.width / unit_slab.get_cell()[0, 0])
self.ny = int(self.height / unit_slab.get_cell()[1, 1])
if self.ny % 2 == 1:
self.ny += 1
#self.ny = 1
print 'number of unit cells', self.nx, self.ny
crack_slab = unit_slab * (self.nx, self.ny, self.nz)
write('ref_slab.xyz', crack_slab)
crack_slab.center(self.vacuum, axis=0)
crack_slab.center(self.vacuum, axis=1)
crack_slab.positions[:, 0] -= crack_slab.positions[:, 0].mean()
crack_slab.positions[:, 1] -= crack_slab.positions[:, 1].mean()
self.orig_width = (crack_slab.positions[:, 0].max() -
crack_slab.positions[:, 0].min())
self.orig_height = (crack_slab.positions[:, 1].max() -
crack_slab.positions[:, 1].min())
print((
'Made slab with %d atoms, original width and height: %.1f x %.1f A^2'
% (len(crack_slab), self.orig_width, self.orig_height)))
top = crack_slab.positions[:, 1].max()
bottom = crack_slab.positions[:, 1].min()
left = crack_slab.positions[:, 0].min()
right = crack_slab.positions[:, 0].max()
#Constrain top and bottom layer of atoms:
fixed_mask = ((abs(crack_slab.positions[:, 1] - top) < 1.0) |
(abs(crack_slab.positions[:, 1] - bottom) < 1.0))
const = FixAtoms(mask=fixed_mask)
crack_slab.set_constraint(const)
#Strain is a dimensionless ratio we require elastic tensor
#to translate the initial energy flow to the tip into a strain.
self.E = youngs_modulus(self.cij, self.cleavage_plane)
self.nu = poisson_ratio(self.cij, self.cleavage_plane,
self.crack_direction)
self.strain = G_to_strain(self.initial_G, self.E, self.nu,
self.orig_height)
seed = left + self.crack_seed_length
tip = left + self.crack_seed_length + self.strain_ramp_length
xpos = crack_slab.positions[:, 0]
ypos = crack_slab.positions[:, 1]
crack_slab.positions[:, 1] += thin_strip_displacement_y(
xpos, ypos, self.strain, seed, tip)
write('crack_slab_init.xyz', crack_slab)
print('Applied initial load: strain=%.4f, G=%.2f J/m^2' %
(self.strain, self.initial_G / (units.J / units.m**2)))
pot_dir = os.environ['POTDIR']
crack_slab.set_calculator(pot)
#Initial crack pos
print 'crack_pos before relaxations'
print find_crack_tip_stress_field(crack_slab, calc=mm_pot)
print('Relaxing slab...')
slab_opt = PreconFIRE(crack_slab)
slab_opt.run(fmax=self.relax_fmax)
return crack_slab
