def build_surface(self, pot, size=(1, 1, 1)):
"""
Create an equivalent surface unit cell for the fracture system.
"""
if self.symbol == 'Si':
unit_slab = Diamond(directions=[
self.crack_direction, self.cleavage_plane, self.crack_front
],
size=size,
symbol=self.symbol,
pbc=True,
latticeconstant=self.a0)
elif self.symbol == 'Fe':
unit_slab = BodyCenteredCubic(directions=[
self.crack_direction, self.cleavage_plane, self.crack_front
],
size=size,
symbol='Fe',
pbc=(1, 1, 1),
latticeconstant=self.a0)
# Does this work for more than 2 atoms?
unit_slab.info['adsorbate_info'] = None
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())
surface = unit_slab.copy()
surface.center(vacuum=self.vacuum, axis=1)
surface.set_calculator(pot)
return surface
def diamond_110_001(el, a0, n, crack_surface=[1,1,0], crack_front=[0,0,1],
skin_x=1.0, skin_y=1.0, vac=5.0):
nx, ny, nz = n
third_dir = np.cross(crack_surface, crack_front)
directions = [ third_dir, crack_surface, crack_front ]
if np.linalg.det(directions) < 0:
third_dir = -third_dir
directions = [ third_dir, crack_surface, crack_front ]
a = Diamond(el, latticeconstant = a0, size = [ nx,ny,nz ],
directions = directions)
sx, sy, sz = a.get_cell().diagonal()
a.translate([a0/100,a0/100,a0/100])
a.set_scaled_positions(a.get_scaled_positions())
a.center()
lx = skin_x*sx/nx
ly = skin_y*sy/ny
r = a.get_positions()
g = np.where(
np.logical_or(
np.logical_or(
np.logical_or(
r[:, 0] < lx, r[:, 0] > sx-lx),
r[:, 1] < ly),
r[:, 1] > sy-ly),
np.zeros(len(a), dtype=int),
np.ones(len(a), dtype=int))
a.set_array('groups', g)
a.set_cell([sx+2*vac, sy+2*vac, sz])
a.translate([vac, vac, 0.0])
a.set_pbc([False, False, True])
return a
def build_unit_slab(self, size=(1, 1, 1)):
"""
Initialize the unit slab for the given crack geometry.
Currently supports silicon and Fe.
"""
if self.symbol == 'Si':
unit_slab = Diamond(directions=[
self.crack_direction, self.cleavage_plane, self.crack_front
],
size=size,
symbol=self.symbol,
pbc=True,
latticeconstant=self.a0)
elif self.symbol == 'Fe':
unit_slab = BodyCenteredCubic(directions=[
self.crack_direction, self.cleavage_plane, self.crack_front
],
size=size,
symbol='Fe',
pbc=(1, 1, 1),
latticeconstant=self.a0)
print 'Number atoms in unit slab', len(unit_slab)
unit_slab.info['adsorbate_info'] = None
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())
pot_dir = os.environ['POTDIR']
pot_file = os.path.join(pot_dir, self.param_file)
print pot_file
print self.mm_init_args
#pot = Potential(self.mm_init_args, param_filename = pot_file)
#pot = Potential("IP EAM_ErcolAd do_rescale_r=T r_scale=1.00894848312" , param_filename = "/Users/lambert/pymodules/imeall/imeall/potentials/PotBH.xml")
#unit_slab.set_calculator(pot)
return unit_slab
def dia_111_glide(sym, a0):
sym = string2symbols(sym)
if len(sym) == 1:
a = Diamond(sym[0],
size=[nx, nx, nz],
latticeconstant=a0,
directions=[[1, -1, 0], [1, 1, -2], [1, 1, 1]])
else:
a = B3(sym,
size=[nx, nx, nz],
latticeconstant=a0,
directions=[[1, -1, 0], [1, 1, -2], [1, 1, 1]])
sx, sy, sz = a.get_cell().diagonal()
a.translate([sx / (12 * nx), sy / (4 * nx), sz / (12 * nz) - 0.2])
a.set_scaled_positions(a.get_scaled_positions() % 1.0)
return a
def dia_111_pandey(sym, a0, nx=nx, ny=nx, nz=nz):
"""2x1 Pandey reconstructed (111) surface."""
sym = string2symbols(sym)
if len(sym) == 1:
a = Diamond(sym[0],
size = [nx, ny, nz],
latticeconstant = a0,
directions=[ [1,-1,0], [1,1,-2], [1,1,1] ]
)
else:
a = B3(sym,
size = [nx, ny, nz],
latticeconstant = a0,
directions=[ [1,-1,0], [1,1,-2], [1,1,1] ]
)
sx, sy, sz = a.get_cell().diagonal()
a.translate([sx/(12*nx), sy/(4*ny), sz/(6*nz)])
a.set_scaled_positions(a.get_scaled_positions()%1.0)
bulk = a.copy()
bondlen = a0*sqrt(3)/4
x, y, z = a.positions.T
mask = np.abs(z-z.max()) < 0.1*a0
top1, top2 = np.arange(len(a))[mask].reshape(-1, 2).T
mask = np.logical_and(np.abs(z-z.max()) < bondlen, np.logical_not(mask))
topA, topB = np.arange(len(a))[mask].reshape(-1, 2).T
y[topA] += bondlen/3
y[topB] -= bondlen/3
y[top1] += bondlen
x[top1] += a.cell[0,0]/(2*nx)
x[top2] += a.cell[0,0]/(2*nx)
mask = np.abs(z-z.min()) < 0.1*a0
bot1, bot2 = np.arange(len(a))[mask].reshape(-1, 2).T
mask = np.logical_and(np.abs(z-z.min()) < bondlen, np.logical_not(mask))
botA, botB = np.arange(len(a))[mask].reshape(-1, 2).T
y[botA] += bondlen/3
y[botB] -= bondlen/3
y[bot2] -= bondlen
x[bot2] += a.cell[0,0]/(2*nx)
x[bot1] += a.cell[0,0]/(2*nx)
a.set_scaled_positions(a.get_scaled_positions()%1.0)
return bulk, a
def diamond_110_110(el, a0, n, crack_surface=[1,1,0],
crack_front=[1,-1,0],
skin_x=0.5, skin_y=1.0,
central_x=-1.0, central_y=-1.0,
vac=5.0):
nx, ny, nz = n
third_dir = np.cross(crack_surface, crack_front)
a = Diamond(el,
latticeconstant = a0,
size = [nx, ny, nz],
directions = [third_dir, crack_surface, crack_front]
)
sx, sy, sz = a.get_cell().diagonal()
a.translate([sx/(8*nx), sy/(4*ny), sz/(4*nz)])
a.set_scaled_positions(a.get_scaled_positions())
skin_x = skin_x*sx/nx
skin_y = skin_y*sy/ny
r = a.get_positions()
g = np.where(
np.logical_or(
np.logical_or(
np.logical_or(
r[:, 0] < skin_x, r[:, 0] > sx-skin_x),
r[:, 1] < skin_y),
r[:, 1] > sy-skin_y),
np.zeros(len(a), dtype=int),
np.ones(len(a), dtype=int))
g = np.where(
np.logical_or(
np.logical_or(
np.logical_or(
r[:, 0] < sx/2-central_x, r[:, 0] > sx/2+central_x),
r[:, 1] < sy/2-central_y),
r[:, 1] > sy/2+central_y),
g,
2*np.ones(len(a), dtype=int))
a.set_array('groups', g)
a.set_cell([sx+2*vac, sy+2*vac, sz])
a.translate([vac, vac, 0.0])
a.set_pbc([False, False, True])
return a
def dia_111_glide(sym, a0):
sym = string2symbols(sym)
if len(sym) == 1:
a = Diamond(sym[0],
size = [nx, nx, nz],
latticeconstant = a0,
directions=[ [1,-1,0], [1,1,-2], [1,1,1] ]
)
else:
a = B3(sym,
size = [nx, nx, nz],
latticeconstant = a0,
directions=[ [1,-1,0], [1,1,-2], [1,1,1] ]
)
sx, sy, sz = a.get_cell().diagonal()
a.translate([sx/(12*nx), sy/(4*nx), sz/(12*nz)-0.2])
a.set_scaled_positions(a.get_scaled_positions()%1.0)
return a
def build_surface(self,pot, size=(1,1,1)):
"""
Create an equivalent surface unit cell for the fracture system.
"""
if self.symbol=='Si':
unit_slab = Diamond(directions = [self.crack_direction, self.cleavage_plane, self.crack_front],
size = size, symbol=self.symbol, pbc=True, latticeconstant= self.a0)
elif self.symbol=='Fe':
unit_slab = BodyCenteredCubic(directions=[self.crack_direction, self.cleavage_plane, self.crack_front],
size=size, symbol='Fe', pbc=(1,1,1),
latticeconstant=self.a0)
# Does this work for more than 2 atoms?
unit_slab.info['adsorbate_info'] = None
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())
surface = unit_slab.copy()
surface.center(vacuum=self.vacuum, axis=1)
surface.set_calculator(pot)
return surface
def build_unit_slab(self, size=(1,1,1)):
"""
Initialize the unit slab for the given crack geometry.
Currently supports silicon and Fe.
"""
if self.symbol=='Si':
unit_slab = Diamond(directions = [self.crack_direction, self.cleavage_plane, self.crack_front],
size = size, symbol=self.symbol, pbc=True, latticeconstant= self.a0)
elif self.symbol=='Fe':
unit_slab = BodyCenteredCubic(directions=[self.crack_direction, self.cleavage_plane, self.crack_front],
size=size, symbol='Fe', pbc=(1,1,1),
latticeconstant=self.a0)
print 'Number atoms in unit slab', len(unit_slab)
unit_slab.info['adsorbate_info'] = None
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())
pot_dir = os.environ['POTDIR']
pot_file = os.path.join(pot_dir, self.param_file)
print pot_file
print self.mm_init_args
#pot = Potential(self.mm_init_args, param_filename = pot_file)
#pot = Potential("IP EAM_ErcolAd do_rescale_r=T r_scale=1.00894848312" , param_filename = "/Users/lambert/pymodules/imeall/imeall/potentials/PotBH.xml")
#unit_slab.set_calculator(pot)
return unit_slab
assert (abs(E_r - E) / units.GPa < 1e-3)
nu_r = -S_r[1, 2] / S_r[1, 1]
print('Possion ratio from C_r: %.3f' % (nu_r))
assert (abs(nu_r - nu) < 1e-3)
print('Unit slab with %d atoms per unit cell:' % len(unit_slab))
print(unit_slab.cell)
print('')
# center vertically half way along the vertical bond between atoms 0 and 1
unit_slab.positions[:, 1] += (unit_slab.positions[1, 1] -
unit_slab.positions[0, 1]) / 2.0
# map positions back into unit cell
unit_slab.set_scaled_positions(unit_slab.get_scaled_positions())
# Make a surface unit cell by repllcating and adding some vaccum along y
surface = unit_slab * [1, params.surf_ny, 1]
surface.center(params.vacuum, axis=1)
# ********** Surface energy ************
# Calculate surface energy per unit area
surface.set_calculator(params.calc)
if hasattr(params, 'relax_bulk') and params.relax_bulk:
print('Minimising surface unit cell...')
opt = FIRE(surface)
opt.run(fmax=params.bulk_fmax)
assert (abs(E_r - E)/units.GPa < 1e-3)
nu_r = -S_r[1,2]/S_r[1,1]
print('Possion ratio from C_r: %.3f' % (nu_r))
assert (abs(nu_r - nu) < 1e-3)
print('Unit slab with %d atoms per unit cell:' % len(unit_slab))
print(unit_slab.cell)
print('')
# center vertically half way along the vertical bond between atoms 0 and 1
unit_slab.positions[:, 1] += (unit_slab.positions[1, 1] -
unit_slab.positions[0, 1]) / 2.0
# map positions back into unit cell
unit_slab.set_scaled_positions(unit_slab.get_scaled_positions())
# Make a surface unit cell by repllcating and adding some vaccum along y
surface = unit_slab * [1, params.surf_ny, 1]
surface.center(params.vacuum, axis=1)
# ********** Surface energy ************
# Calculate surface energy per unit area
surface.set_calculator(params.calc)
if hasattr(params, 'relax_bulk') and params.relax_bulk:
print('Minimising surface unit cell...')
opt = FIRE(surface)
opt.run(fmax=params.bulk_fmax)
