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
<params>
<LMTO_TBE_params n_types="2" control_file="ctrl.fe">
<per_type_data type="1" atomic_num="26"/>
<per_type_data type="2" atomic_num="1"/>
</LMTO_TBE_params>
</params>""")
#If there is an initial strain energy increment that here:
pot.print_()
screw_slab_unit.write('screw_unitcell.xyz')
screw_slab_unit.set_calculator(pot)
#Elastic constants are disabled until we have tight binding operational.
if calc_elastic_constants and dyn_type != 'LOTF':
cij = pot.get_elastic_constants(screw_slab_unit)
print 'ELASTIC CONSTANTS'
print ((cij / units.GPa).round(2))
E = youngs_modulus(cij, y)
nu = poisson_ratio(cij, y, x)
print 'Youngs Modulus: ', E/units.GPa,'Poisson Ratio: ', nu
print 'Effective elastic modulus E: ', E/(1.-nu**2)
print 'Loading Structure File:', '{0}.xyz'.format(input_file)
defect = Atoms('{0}.xyz'.format(input_file))
top = defect.positions[:,1].max()
bottom = defect.positions[:,1].min()
left = defect.positions[:,0].min()
right = defect.positions[:,0].max()
orig_height = (defect.positions[:,1].max()-defect.positions[:,1].min())
#Attaching Properties to atoms object
if calc_elastic_constants:
defect.info['YoungsModulus'] = E
<params>
<LMTO_TBE_params n_types="2" control_file="ctrl.fe">
<per_type_data type="1" atomic_num="26"/>
<per_type_data type="2" atomic_num="1"/>
</LMTO_TBE_params>
</params>""")
#If there is an initial strain energy increment that here:
pot.print_()
screw_slab_unit.write('screw_unitcell.xyz')
screw_slab_unit.set_calculator(pot)
#Elastic constants are disabled until we have tight binding operational.
if calc_elastic_constants and dyn_type != 'LOTF':
cij = pot.get_elastic_constants(screw_slab_unit)
print 'ELASTIC CONSTANTS'
print((cij / units.GPa).round(2))
E = youngs_modulus(cij, y)
nu = poisson_ratio(cij, y, x)
print 'Youngs Modulus: ', E / units.GPa, 'Poisson Ratio: ', nu
print 'Effective elastic modulus E: ', E / (1. - nu**2)
print 'Loading Structure File:', '{0}.xyz'.format(input_file)
defect = Atoms('{0}.xyz'.format(input_file))
top = defect.positions[:, 1].max()
bottom = defect.positions[:, 1].min()
left = defect.positions[:, 0].min()
right = defect.positions[:, 0].max()
orig_height = (defect.positions[:, 1].max() - defect.positions[:, 1].min())
#Attaching Properties to atoms object
if calc_elastic_constants:
defect.info['YoungsModulus'] = E
a0 = si_bulk.cell[0, 0]
print('Lattice constant %.3f A\n' % a0)
# make a new bulk cell with correct a0 (so that off-diagonal lattice values are exactly zero)
si_bulk = bulk('Si', 'diamond', a=a0, cubic=True)
si_bulk.set_calculator(mm_pot)
# ******* Find elastic constants *******
# Get 6x6 matrix of elastic constants C_ij
c = mm_pot.get_elastic_constants(si_bulk)
print('Elastic constants (GPa):')
print((c / units.GPa).round(0))
print('')
E = youngs_modulus(c, cleavage_plane)
print('Young\'s modulus %.1f GPa' % (E / units.GPa))
nu = poisson_ratio(c, cleavage_plane, crack_direction)
print('Poisson ratio % .3f\n' % nu)
# **** Setup crack slab unit cell ******
print_crack_system(crack_direction, cleavage_plane, crack_front)
# now, we build system aligned with requested crystallographic orientation
unit_slab = Diamond(directions=[crack_direction,
cleavage_plane,
crack_front],
size=(1, 1, 1),
symbol='Si',
pbc=True,
crack_seed_length = 40.0*units.Ang # Length of seed crack
strain_ramp_length = 30.0*units.Ang # Distance over which strain is ramped up
initial_G = 5.0*(units.J/units.m**2) # Initial energy flow to crack tip
relax_fmax = 0.025*units.eV/units.Ang # Maximum force criteria for relaxation
output_file = 'crack.xyz' # File to which structure will be written
set_fortran_indexing(False)
si_bulk = bulk('Si', 'diamond', a=5.431, cubic=True)
mm_pot = Potential("IP SW")
si_bulk.set_calculator(mm_pot)
c = mm_pot.get_elastic_constants(si_bulk)
E = youngs_modulus(c, cleavage_plane)
nu = poisson_ratio(c, cleavage_plane, crack_direction)
unit_slab = Diamond(directions=[crack_direction,
cleavage_plane,
crack_front],
size=(1, 1, 1),
symbol='Si',
pbc=True,
latticeconstant=5.431)
unit_slab.positions[:, 1] += (unit_slab.positions[1, 1] -
unit_slab.positions[0, 1]) / 2.0
unit_slab.set_scaled_positions(unit_slab.get_scaled_positions())
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