def dia_100_2x1(sym, a0):
sym = string2symbols(sym)
if len(sym) == 1:
a = Diamond(sym[0],
size = [2*nx, nx, nz],
latticeconstant = a0,
directions=[ [1,-1,0], [1,1,0], [0,0,1] ]
)
else:
a = B3(sym,
size = [2*nx, nx, nz],
latticeconstant = a0,
directions=[ [1,-1,0], [1,1,0], [0,0,1] ]
)
sx, sy, sz = a.get_cell().diagonal()
a.translate([sx/(8*nx), sy/(8*nx), sz/(8*nz)])
bulk = a.copy()
for i in a:
if i.z < sz/(4*nz) or i.z > sz-sz/(4*nz):
if i.x < sx/2:
i.x = i.x+0.5
else:
i.x = i.x-0.5
return bulk, a
def test_sqlite(testdir):
CP = Checkpoint('checkpoints.db')
a = Diamond('Si', size=[2, 2, 2])
a = CP(op1)(a, 1.0)
op1a = a.copy()
a, ra = CP(op2)(a, 2.0)
op2a = a.copy()
op2ra = ra.copy()
CP = Checkpoint('checkpoints.db')
a = Diamond('Si', size=[2, 2, 2])
a = CP(op1)(a, 1.0)
assert a == op1a
a, ra = CP(op2)(a, 2.0)
assert a == op2a
assert(np.abs(ra - op2ra).max() < 1e-5)
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 test_dsygv_dgelsd(self):
a = Diamond('C', size=[4,4,4])
b = a.copy()
b.positions += (np.random.random(b.positions.shape)-0.5)*0.1
i, j = neighbour_list("ij", b, 1.85)
dr_now = mic(b.positions[i] - b.positions[j], b.cell)
dr_old = mic(a.positions[i] - a.positions[j], a.cell)
dgrad1 = get_delta_plus_epsilon_dgesv(len(b), i, dr_now, dr_old)
dgrad2 = get_delta_plus_epsilon(len(b), i, dr_now, dr_old)
self.assertArrayAlmostEqual(dgrad1, dgrad2)
def test_sqlite():
print('test_single_file')
try:
os.remove('checkpoints.db')
except OSError:
pass
CP = Checkpoint('checkpoints.db')
a = Diamond('Si', size=[2, 2, 2])
a = CP(op1)(a, 1.0)
op1a = a.copy()
a, ra = CP(op2)(a, 2.0)
op2a = a.copy()
op2ra = ra.copy()
CP = Checkpoint('checkpoints.db')
a = Diamond('Si', size=[2, 2, 2])
a = CP(op1)(a, 1.0)
assert a == op1a
a, ra = CP(op2)(a, 2.0)
assert a == op2a
assert(np.abs(ra - op2ra).max() < 1e-5)
def test_sqlite(self):
print('test_single_file')
try:
os.remove('checkpoints.db')
except OSError:
pass
CP = Checkpoint('checkpoints.db')
a = Diamond('Si', size=[2, 2, 2])
a = CP(self.op1)(a, 1.0)
op1a = a.copy()
a, ra = CP(self.op2)(a, 2.0)
op2a = a.copy()
op2ra = ra.copy()
CP = Checkpoint('checkpoints.db')
a = Diamond('Si', size=[2, 2, 2])
a = CP(self.op1)(a, 1.0)
self.assertEqual(a, op1a)
a, ra = CP(self.op2)(a, 2.0)
self.assertEqual(a, op2a)
self.assert_(np.abs(ra - op2ra).max() < 1e-5)
def test_sqlite(self):
print('test_single_file')
try:
os.remove('checkpoints.db')
except OSError:
pass
CP = Checkpoint('checkpoints.db')
a = Diamond('Si', size=[2,2,2])
a = CP(self.op1)(a, 1.0)
op1a = a.copy()
a, ra = CP(self.op2)(a, 2.0)
op2a = a.copy()
op2ra = ra.copy()
CP = Checkpoint('checkpoints.db')
a = Diamond('Si', size=[2,2,2])
a = CP(self.op1)(a, 1.0)
self.assertAtomsAlmostEqual(a, op1a)
a, ra = CP(self.op2)(a, 2.0)
self.assertAtomsAlmostEqual(a, op2a)
self.assertArrayAlmostEqual(ra, op2ra)
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 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
ase.io.write(sys.stdout, bulk, format='extxyz')
print 'expanded cell energy', eexp
e_form = 0.5*(eexp - ebulk) / np.linalg.norm(np.cross(bulk.cell[0,:],bulk.cell[1,:]))
print 'unrelaxed 110 surface formation energy', e_form
return e_form
# dictionary of computed properties - this is output of this test, to
# be compared with other models
n_steps = 35
max_opening = 3.5
openings = []
es = []
for i in range(n_steps + 1):
opening = float(i)/float(n_steps)*max_opening
openings.append(opening)
bulk_copy = bulk.copy()
bulk_copy.set_calculator(model.calculator)
es.append(surface_energy(bulk_copy, 2.0, opening))
print "openings ", openings
print "es ", es
from scipy import interpolate
spline = interpolate.splrep(openings, es, s=0)
stresses = [x for x in interpolate.splev(openings, spline, der=1)]
print "stresses ", stresses
properties = {'surface_decohesion_unrelaxed_opening': openings, 'surface_decohesion_unrelaxed_energy' : es, 'surface_decohesion_unrelaxed_stress' : stresses}
# You could check elastic constants of this rotated system:
# should lead to same Young's modulus and Poisson ratio
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 adding some vaccum along y
surface = unit_slab.copy()
surface.center(vacuum, axis=1)
# ********** Surface energy ************
# Calculate surface energy per unit area
surface.set_calculator(mm_pot)
E_surf = surface.get_potential_energy()
E_per_atom_bulk = si_bulk.get_potential_energy() / len(si_bulk)
area = surface.get_volume() / surface.cell[1, 1]
gamma = ((E_surf - E_per_atom_bulk * len(surface)) /
(2.0 * area))
print('Surface energy of %s surface %.4f J/m^2\n' %
(cleavage_plane, gamma / (units.J / units.m ** 2)))
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())
surface = unit_slab.copy()
surface.center(vacuum, axis=1)
surface.set_calculator(mm_pot)
E_surf = surface.get_potential_energy()
E_per_atom_bulk = si_bulk.get_potential_energy() / len(si_bulk)
area = surface.get_volume() / surface.cell[1, 1]
gamma = ((E_surf - E_per_atom_bulk * len(surface)) /
(2.0 * area))
nx = int(width / unit_slab.cell[0, 0])
ny = int(height / unit_slab.cell[1, 1])
# make sure ny is even so slab is centered on a bond
if ny % 2 == 1:
else:
bulk.set_calculator(model.calculator)
bulk = relax_atoms_cell(bulk, tol=tol, traj_file=None)
print 'bulk reference len=%d cell=%r' % (len(bulk), bulk.cell)
bulk *= (N, N, N)
bulk.set_calculator(model.calculator)
e_bulk_per_atom = bulk.get_potential_energy() / len(bulk)
print 'e_bulk_per_atom', e_bulk_per_atom
if remove_index == 'center':
half_cell = np.diag(bulk.cell) / 2.
remove_index = ((bulk.positions - half_cell)**2).sum(axis=1).argmin()
initial = bulk.copy()
orig_pos = initial.get_positions()[remove_index, :]
nl = NeighborList([a0 * sqrt(3.0) / 4 * 0.6] * len(initial),
self_interaction=False,
bothways=True)
nl.update(initial)
indices, offsets = nl.get_neighbors(remove_index)
remove_index_f = None
initial.arrays['ind'] = array([i for i in range(len(initial))])
offset_factor = 0.13
for i, offset in zip(indices, offsets):
ri = initial.positions[remove_index] - (initial.positions[i] +
dot(offset, initial.get_cell()))
if remove_index_f is None:
remove_index_f = i
