def extend_strip(atoms, a, N, M, vacuum):
x = atoms.positions[:, 0]
left = x.min()
width = x.max() - x.min()
tip_x = atoms.info['tip_x']
if tip_x < left + 0.6 * width:
# only need to extend strip when crack gets near end
return False
print('tip_x (%.2f) > left + 0.75*width (%.2f)' %
(tip_x, left + 0.75 * width))
# extra material for pasting onto end
a = atoms.get_calculator().parameters['a']
extra = triangular_lattice_slab(a, M, N)
# apply uniform strain and append to slab
strain = get_strain(atoms)
extra.center(vacuum, axis=1)
fix = atoms.get_array('fix')
extra.positions[:, 0] += atoms.positions[fix, 0].max() + a / 2.0
extra.positions[:, 1] -= extra.positions[:, 1].mean()
extra.positions[:, 1] *= (1.0 + strain)
print('Adding %d atoms' % len(extra))
atoms += extra
atoms.set_constraint([])
discard = atoms.positions[:, 0].argsort()[:len(extra)]
print('Discarding %d atoms' % len(discard))
del atoms[discard]
return True
def extend_strip(atoms, a, N, M, vacuum):
x = atoms.positions[:, 0]
left = x.min()
width = x.max() - x.min()
tip_x = atoms.info['tip_x']
if tip_x < left + 0.6*width:
# only need to extend strip when crack gets near end
return False
print 'tip_x (%.2f) > left + 0.75*width (%.2f)' % (tip_x, left + 0.75*width)
# extra material for pasting onto end
a = atoms.get_calculator().parameters['a']
extra = triangular_lattice_slab(a, M, N)
# apply uniform strain and append to slab
strain = get_strain(atoms)
extra.center(vacuum, axis=1)
fix = atoms.get_array('fix')
extra.positions[:, 0] += atoms.positions[fix, 0].max() + a/2.0
extra.positions[:, 1] -= extra.positions[:, 1].mean()
extra.positions[:, 1] *= (1.0 + strain)
print 'Adding %d atoms' % len(extra)
atoms += extra
atoms.set_constraint([])
discard = atoms.positions[:, 0].argsort()[:len(extra)]
print 'Discarding %d atoms' % len(discard)
del atoms[discard]
return True
def find_crack_tip(atoms, dt=None, store=True, results=None):
"""
Return atom at the crack tip and its x-coordinate
Crack tip is defined to be location of rightmost atom
whose nearest neighbour is at distance > 2.5*a
"""
calc = atoms.get_calculator()
a = calc.parameters['a']
rc = calc.parameters['rc']
i = neighbour_list('i', atoms, rc)
nn = np.bincount(i) # number of nearest neighbours, equal to 6 in bulk
x = atoms.positions[:, 0]
y = atoms.positions[:, 1]
bottom = y.min()
left = x.min()
width = x.max() - x.min()
height = y.max() - y.min()
old_tip_x = atoms.info.get('tip_x', left + 0.3*width)
# crack cannot have advanced more than c_R*dt
if dt is not None:
cl, ct, cR = calc.get_wave_speeds(atoms)
tip_max_x = old_tip_x + 10.0*cR*dt # FIXME definition of cR seems wrong, shouldn't need factor of 10 here...
else:
tip_max_x = left + 0.8*width
broken = ((nn != 6) &
(x > left + 0.2*width) & (x < tip_max_x) &
(y > bottom + 0.1*height) & (y < bottom + 0.9*height))
index = atoms.positions[broken, 0].argmax()
tip_atom = broken.nonzero()[0][index]
tip_x = atoms.positions[tip_atom, 0]
strain = get_strain(atoms)
eps_G = atoms.info['eps_G']
print 'tip_x: %.3f strain: %.4f delta: %.3f' % (tip_x, strain, strain/eps_G)
if store:
atoms.info['tip_atom'] = tip_atom
atoms.info['tip_x'] = tip_x
if results is not None:
results.append(tip_x)
return (tip_atom, tip_x, broken)
def find_crack_tip(atoms, dt=None, store=True, results=None):
"""
Return atom at the crack tip and its x-coordinate
Crack tip is defined to be location of rightmost atom
whose nearest neighbour is at distance > 2.5*a
"""
calc = atoms.get_calculator()
a = calc.parameters['a']
rc = calc.parameters['rc']
i = neighbour_list('i', atoms, rc)
nn = np.bincount(i) # number of nearest neighbours, equal to 6 in bulk
x = atoms.positions[:, 0]
y = atoms.positions[:, 1]
bottom = y.min()
left = x.min()
width = x.max() - x.min()
height = y.max() - y.min()
old_tip_x = atoms.info.get('tip_x', left + 0.3 * width)
# crack cannot have advanced more than c_R*dt
if dt is not None:
cl, ct, cR = calc.get_wave_speeds(atoms)
tip_max_x = old_tip_x + 10.0 * cR * dt # FIXME definition of cR seems wrong, shouldn't need factor of 10 here...
else:
tip_max_x = left + 0.8 * width
broken = ((nn != 6) & (x > left + 0.2 * width) & (x < tip_max_x) &
(y > bottom + 0.1 * height) & (y < bottom + 0.9 * height))
index = atoms.positions[broken, 0].argmax()
tip_atom = broken.nonzero()[0][index]
tip_x = atoms.positions[tip_atom, 0]
strain = get_strain(atoms)
eps_G = atoms.info['eps_G']
print('tip_x: %.3f strain: %.4f delta: %.3f' %
(tip_x, strain, strain / eps_G))
if store:
atoms.info['tip_atom'] = tip_atom
atoms.info['tip_x'] = tip_x
if results is not None:
results.append(tip_x)
return (tip_atom, tip_x, broken)
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)12.4f%(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'] = get_temperature(atoms)
atoms.info['strain'] = get_strain(atoms)
# FIXME no local virial in TS, need another way to track the crack
atoms.info['crack_pos_x'] = 0.
atoms.info['d_crack_pos_x'] = 0.
print log_format % atoms.info
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_tip_stress_field(atoms)
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 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_tip_stress_field(atoms)
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 find_crack_tip(atoms,
coord=None,
d=None,
tipxfile=None,
cout=None,
dt=None,
store=True,
results=None,
siv=False):
"""
Return atom at the crack tip and its x-coordinate
Crack tip is defined to be location of rightmost atom
whose nearest neighbour is at distance > 2.5*a
"""
calc = atoms.get_calculator()
a = calc.parameters['a']
rc = calc.parameters['rc']
i = neighbour_list('i', atoms, rc)
nn = np.bincount(i) # number of nearest neighbours, equal to 6 in bulk
x = atoms.positions[:, 0]
y = atoms.positions[:, 1]
bottom = y.min()
left = x.min()
width = x.max() - x.min()
height = y.max() - y.min()
old_tip_x = atoms.info.get('tip_x', left + 0.3 * width)
"""Function to print the potential, kinetic and total energy"""
epot = atoms.get_potential_energy() / len(atoms)
ekin = atoms.get_kinetic_energy() / len(atoms)
# print('Energy per atom: Epot = %.3feV Ekin = %.3feV (T=%3.0fK) '
# 'Etot = %.3feV' % (epot, ekin, ekin / (1.5 * units.kB), epot + ekin))
T = ekin / (1.5 * units.kB)
# crack cannot have advanced more than c_R*dt
if dt is not None:
cl, ct, cR = calc.get_wave_speeds(atoms)
#tip_max_x = old_tip_x + 10.0*cR*dt # FIXME definition of cR seems wrong, shouldn't need factor of 10 here...
tip_max_x = old_tip_x + cR * dt # FIXME unit conversion included now
else:
tip_max_x = left + 0.8 * width
broken = ((nn != 6) & (x > left + 0.2 * width) & (x < tip_max_x) &
(y > bottom + 0.1 * height) & (y < bottom + 0.9 * height))
index = atoms.positions[broken, 0].argmax()
tip_atom = broken.nonzero()[0][index]
tip_x = atoms.positions[tip_atom, 0]
tip_y = atoms.positions[tip_atom, 1]
coord.append([tip_x, tip_y])
#! d is distance
if len(coord) >= 2:
d.append(((coord[-1][0] - coord[-2][0])**2 +
(coord[-1][1] - coord[-2][1])**2)**(0.5))
total_d = sum(d)
strain = get_strain(atoms)
eps_G = atoms.info['eps_G']
print('tip_x: %.3f tip_y: %.0f d: %.2f T: %.1f strain: %.4f delta: %.3f' %
(tip_x, tip_y, total_d, T, strain, strain / eps_G))
# print(atoms.get_temperature())
#! No need to write anything if set_initial_velocity() calls this function
if not siv:
#!saving tip_x to text file
tipxfile.write(str(tip_x) + ',' + str(strain) + '\n')
#!saving console output
cout.write(
'tip_x: %.3f tip_y: %.3f d: %.3f T: %d strain: %.4f delta: %.3f \n'
% (tip_x, tip_y, total_d, T, strain, strain / eps_G))
if store:
atoms.info['tip_atom'] = tip_atom
atoms.info['tip_x'] = tip_x
if results is not None:
results.append(tip_x)
return (tip_atom, tip_x, broken)
traj_file = open('traj-m-6r.xyz', 'w')
minimiser = FIRE(atoms, restart='hess.traj')
def trajectory_write():
ase.io.extxyz.write_xyz(traj_file, atoms)
# swap is an array of atom indices that have to be sent in opposite direction wrt
# what thin_strip_displacement_y would do.
swap = np.loadtxt('swap_topbottom_atoms.csv')
for i in range(1000):
minimiser.run(fmax=params.relax_fmax)
trajectory_write()
# Find initial position of crack tip
#crack_pos = find_tip_stress_field(crack_slab, calc=params.calc)
#print 'Found crack tip at position %s' % crack_pos
atoms.info['strain'] = get_strain(atoms)
strain = atoms.info['strain']
print("Strain: %f" % strain)
# update atomic positions
displacement = thin_strip_displacement_y(
atoms.positions[:, 0],
atoms.positions[:, 1],
params.strain_rate * params.timestep,
left + params.crack_seed_length,
left + params.crack_seed_length +
params.strain_ramp_length)
displacement[swap] = -displacement[swap]
atoms.positions[:, 1] += displacement
