def test_anisotropic_near_field_solution(self):
"""
Run an atomistic calculation of a harmonic solid and compare to
continuum solution.
"""
if not atomistica:
print('Atomistica not available. Skipping test.')
return
for nx in [ 8, 16, 32, 64 ]:
for calc, a, C11, C12, C44, surface_energy, bulk_coordination in [
#( atomistica.DoubleHarmonic(k1=1.0, r1=1.0, k2=1.0,
# r2=math.sqrt(2), cutoff=1.6),
# clusters.sc('He', 1.0, [nx,nx,1], [1,0,0], [0,1,0]),
# 3, 1, 1, 0.05, 6 ),
( atomistica.Harmonic(k=1.0, r0=1.0, cutoff=1.3, shift=True),
clusters.fcc('He', math.sqrt(2.0), [nx,nx,1], [1,0,0],
[0,1,0]),
math.sqrt(2), 1.0/math.sqrt(2), 1.0/math.sqrt(2), 0.05, 12)
]:
clusters.set_groups(a, (nx, nx, 1), 0.5, 0.5)
crack = CubicCrystalCrack([1,0,0], [0,1,0], C11, C12, C44)
a.center(vacuum=20.0, axis=0)
a.center(vacuum=20.0, axis=1)
a.set_calculator(calc)
sx, sy, sz = a.cell.diagonal()
tip_x = sx/2
tip_y = sy/2
k1g = crack.k1g(surface_energy)
r0 = a.positions.copy()
u, v = crack.displacements(a.positions[:,0], a.positions[:,1],
tip_x, tip_y, k1g)
a.positions[:,0] += u
a.positions[:,1] += v
g = a.get_array('groups')
a.set_constraint(FixAtoms(mask=g==0))
#ase.io.write('initial_{}.xyz'.format(nx), a, format='extxyz')
x1, y1, z1 = a.positions.copy().T
FIRE(a, logfile=None).run(fmax=1e-3)
x2, y2, z2 = a.positions.T
# Get coordination numbers and find properly coordinated atoms
coord = calc.nl.get_coordination_numbers(calc.particles, 1.1)
mask=coord == bulk_coordination
residual = np.sqrt(((x2-x1)/u)**2 + ((y2-y1)/v)**2)
#a.set_array('residual', residual)
#ase.io.write('final_{}.xyz'.format(nx), a, format='extxyz')
#print(np.max(residual[mask]))
self.assertTrue(np.max(residual[mask]) < 0.2)
def test_elastostatics(self):
eps = 1e-3
for C11, C12, C44, surface_energy, k1 in self.materials:
crack = CubicCrystalCrack([1,0,0], [0,1,0], C11, C12, C44)
k = crack.k1g(surface_energy)*k1
for i in range(10):
x = i+1
y = i+1
# Finite difference approximation of the stress divergence
sxx0x, syy0x, sxy0x = crack.stresses(x-eps, y, 0, 0, k)
sxx0y, syy0y, sxy0y = crack.stresses(x, y-eps, 0, 0, k)
sxx1x, syy1x, sxy1x = crack.stresses(x+eps, y, 0, 0, k)
sxx1y, syy1y, sxy1y = crack.stresses(x, y+eps, 0, 0, k)
divsx = (sxx1x-sxx0x)/(2*eps) + (sxy1y-sxy0y)/(2*eps)
divsy = (sxy1x-sxy0x)/(2*eps) + (syy1y-syy0y)/(2*eps)
# Check that divergence of stress is zero (elastostatic
# equilibrium)
self.assertAlmostEqual(divsx, 0.0, places=3)
self.assertAlmostEqual(divsy, 0.0, places=3)
def test_elastostatics(self):
eps = 1e-3
for C11, C12, C44, surface_energy, k1 in self.materials:
crack = CubicCrystalCrack([1, 0, 0], [0, 1, 0], C11, C12, C44)
k = crack.k1g(surface_energy) * k1
for i in range(10):
x = i + 1
y = i + 1
# Finite difference approximation of the stress divergence
sxx0x, syy0x, sxy0x = crack.stresses(x - eps, y, 0, 0, k)
sxx0y, syy0y, sxy0y = crack.stresses(x, y - eps, 0, 0, k)
sxx1x, syy1x, sxy1x = crack.stresses(x + eps, y, 0, 0, k)
sxx1y, syy1y, sxy1y = crack.stresses(x, y + eps, 0, 0, k)
divsx = (sxx1x - sxx0x) / (2 * eps) + (sxy1y - sxy0y) / (2 *
eps)
divsy = (sxy1x - sxy0x) / (2 * eps) + (syy1y - syy0y) / (2 *
eps)
# Check that divergence of stress is zero (elastostatic
# equilibrium)
self.assertAlmostEqual(divsx, 0.0, places=3)
self.assertAlmostEqual(divsy, 0.0, places=3)
def test_consistency_of_deformation_gradient_and_displacement(self):
eps = 1e-3
for C11, C12, C44, surface_energy, k1 in self.materials:
crack = CubicCrystalCrack([1, 0, 0], [0, 1, 0], C11, C12, C44)
k = crack.k1g(surface_energy) * k1
for i in range(10):
x = i + 1
y = i + 1
F = crack.deformation_gradient(x, y, 0, 0, k)
# Finite difference approximation of deformation gradient
u, v = crack.displacements(x, y, 0, 0, k)
ux0, vx0 = crack.displacements(x - eps, y, 0, 0, k)
uy0, vy0 = crack.displacements(x, y - eps, 0, 0, k)
ux1, vx1 = crack.displacements(x + eps, y, 0, 0, k)
uy1, vy1 = crack.displacements(x, y + eps, 0, 0, k)
du_dx = (ux1 - ux0) / (2 * eps)
du_dy = (uy1 - uy0) / (2 * eps)
dv_dx = (vx1 - vx0) / (2 * eps)
dv_dy = (vy1 - vy0) / (2 * eps)
du_dx += np.ones_like(du_dx)
dv_dy += np.ones_like(dv_dy)
F_num = np.transpose([[du_dx, du_dy], [dv_dx, dv_dy]])
self.assertArrayAlmostEqual(F, F_num, tol=1e-4)
def test_consistency_of_deformation_gradient_and_displacement(self):
eps = 1e-3
for C11, C12, C44, surface_energy, k1 in self.materials:
crack = CubicCrystalCrack([1,0,0], [0,1,0], C11, C12, C44)
k = crack.k1g(surface_energy)*k1
for i in range(10):
x = i+1
y = i+1
F = crack.deformation_gradient(x, y, 0, 0, k)
# Finite difference approximation of deformation gradient
u, v = crack.displacements(x, y, 0, 0, k)
ux0, vx0 = crack.displacements(x-eps, y, 0, 0, k)
uy0, vy0 = crack.displacements(x, y-eps, 0, 0, k)
ux1, vx1 = crack.displacements(x+eps, y, 0, 0, k)
uy1, vy1 = crack.displacements(x, y+eps, 0, 0, k)
du_dx = (ux1-ux0)/(2*eps)
du_dy = (uy1-uy0)/(2*eps)
dv_dx = (vx1-vx0)/(2*eps)
dv_dy = (vy1-vy0)/(2*eps)
du_dx += np.ones_like(du_dx)
dv_dy += np.ones_like(dv_dy)
F_num = np.transpose([[du_dx, du_dy], [dv_dx, dv_dy]])
self.assertArrayAlmostEqual(F, F_num, tol=1e-5)
def test_consistency_of_deformation_gradient_and_stress(self):
for C11, C12, C44, surface_energy, k1 in self.materials:
crack = CubicCrystalCrack([1, 0, 0], [0, 1, 0], C11, C12, C44)
k = crack.k1g(surface_energy) * k1
for i in range(10):
x = np.random.uniform(-10, 10)
y = np.random.uniform(-10, 10)
F = crack.deformation_gradient(x, y, 0, 0, k)
eps = (F + F.T) / 2 - np.eye(2)
sig_x, sig_y, sig_xy = crack.stresses(x, y, 0, 0, k)
eps_xx = crack.crack.a11*sig_x + \
crack.crack.a12*sig_y + \
crack.crack.a16*sig_xy
eps_yy = crack.crack.a12*sig_x + \
crack.crack.a22*sig_y + \
crack.crack.a26*sig_xy
# Factor 1/2 because elastic constants and matrix product are
# expressed in Voigt notation.
eps_xy = (crack.crack.a16*sig_x + \
crack.crack.a26*sig_y + \
crack.crack.a66*sig_xy)/2
self.assertAlmostEqual(eps[0, 0], eps_xx)
self.assertAlmostEqual(eps[1, 1], eps_yy)
self.assertAlmostEqual(eps[0, 1], eps_xy)
def test_consistency_of_deformation_gradient_and_stress(self):
for C11, C12, C44, surface_energy, k1 in self.materials:
crack = CubicCrystalCrack([1,0,0], [0,1,0], C11, C12, C44)
k = crack.k1g(surface_energy)*k1
for i in range(10):
x = np.random.uniform(-10, 10)
y = np.random.uniform(-10, 10)
F = crack.deformation_gradient(x, y, 0, 0, k)
eps = (F+F.T)/2-np.eye(2)
sig_x, sig_y, sig_xy = crack.stresses(x, y, 0, 0, k)
eps_xx = crack.crack.a11*sig_x + \
crack.crack.a12*sig_y + \
crack.crack.a16*sig_xy
eps_yy = crack.crack.a12*sig_x + \
crack.crack.a22*sig_y + \
crack.crack.a26*sig_xy
# Factor 1/2 because elastic constants and matrix product are
# expressed in Voigt notation.
eps_xy = (crack.crack.a16*sig_x + \
crack.crack.a26*sig_y + \
crack.crack.a66*sig_xy)/2
self.assertAlmostEqual(eps[0, 0], eps_xx)
self.assertAlmostEqual(eps[1, 1], eps_yy)
self.assertAlmostEqual(eps[0, 1], eps_xy)
def test_J_integral(self):
if quadrature is None:
print('No scipy.integrate.quadrature. Skipping J-integral test.')
return
for C11, C12, C44, surface_energy, k1 in self.materials:
crack = CubicCrystalCrack([1, 0, 0], [0, 1, 0], C11, C12, C44)
k = crack.k1g(surface_energy) * k1
def polar_path(theta, r=1, x0=0, y0=0):
nx = np.cos(theta)
ny = np.sin(theta)
n = np.transpose([nx, ny])
return r * n - np.array([x0, y0]), n, r
def elliptic_path(theta, r=1, x0=0, y0=0):
rx, ry = r
x = rx * np.cos(theta)
y = ry * np.sin(theta)
nx = ry * np.cos(theta)
ny = rx * np.sin(theta)
ln = np.sqrt(nx**2 + ny**2)
nx /= ln
ny /= ln
ds = np.sqrt((rx * np.sin(theta))**2 + (ry * np.cos(theta))**2)
return np.transpose([x - x0, y - y0]), np.transpose([nx,
ny]), ds
def rectangular_path(t, r):
x = -r * np.ones_like(t)
y = r * (t - 8)
nx = -np.ones_like(t)
ny = np.zeros_like(t)
x = np.where(t < 7, r * (6 - t), x)
y = np.where(t < 7, -r * np.ones_like(t), y)
nx = np.where(t < 7, np.zeros_like(t), nx)
ny = np.where(t < 7, -np.ones_like(t), ny)
x = np.where(t < 5, r * np.ones_like(t), x)
y = np.where(t < 5, r * (4 - t), y)
nx = np.where(t < 5, np.ones_like(t), nx)
ny = np.where(t < 5, np.zeros_like(t), ny)
x = np.where(t < 3, r * (t - 2), x)
y = np.where(t < 3, r * np.ones_like(t), y)
nx = np.where(t < 3, np.zeros_like(t), nx)
ny = np.where(t < 3, np.ones_like(t), ny)
x = np.where(t < 1, -r * np.ones_like(t), x)
y = np.where(t < 1, r * t, y)
nx = np.where(t < 1, -np.ones_like(t), nx)
ny = np.where(t < 1, np.zeros_like(t), ny)
return np.transpose([x, y]), np.transpose([nx, ny]), r
def J(t, path_func=polar_path):
# Position, normal to path, length
pos, n, ds = path_func(t)
x, y = pos.T
nx, ny = n.T
# Stress tensor
sxx, syy, sxy = crack.stresses(x, y, 0, 0, k)
s = np.array([[sxx, sxy], [sxy, syy]]).T
# Deformation gradient and strain tensor
F = crack.deformation_gradient(x, y, 0, 0, k)
eps = (F + F.swapaxes(1, 2)) / 2 - np.identity(2).reshape(
1, 2, 2)
# Strain energy density
W = (s * eps).sum(axis=2).sum(axis=1) / 2
# Note dy == nx*ds
retval = (W * nx - np.einsum('...j,...jk,...k->...', n, s,
F[..., 0, :])) * ds
return retval
eps = 1e-6
for r in [1, 10, 100]:
# Polar path
J_val, J_err = quadrature(
J,
-np.pi + eps,
np.pi - eps,
args=(lambda t: polar_path(t, r)),
)
self.assertAlmostEqual(J_val, 2 * surface_energy, places=2)
# Elliptic path
J_val, J_err = quadrature(
J,
-np.pi + eps,
np.pi - eps,
args=(lambda t: elliptic_path(t, (3 * r, r)), ),
maxiter=200)
self.assertAlmostEqual(J_val, 2 * surface_energy, places=2)
# Elliptic path, shifted in x and y directions off-center
J_val, J_err = quadrature(
J,
-np.pi + eps,
np.pi - eps,
args=(lambda t: elliptic_path(t, (r, 1.5 * r), 0, 0.5), ),
maxiter=200)
self.assertAlmostEqual(J_val, 2 * surface_energy, places=2)
colors = itertools.cycle(colors)
# compute elastic constants
cryst = params.cryst.copy()
cryst.pbc = True
cryst.calc = calc
C, C_err = fit_elastic_constants(cryst,
symmetry=parameter('elastic_symmetry',
'triclinic'))
crk = CubicCrystalCrack(parameter('crack_surface'),
parameter('crack_front'),
Crot=C / GPa)
# Get Griffith's k1.
k1g = crk.k1g(parameter('surface_energy'))
print('Griffith k1 = %f' % k1g)
cluster = params.cluster.copy()
plot_approx = parameter('plot_approx', False)
if plot_approx:
fig, (ax1, ax2) = plt.subplots(2, 1, figsize=(6, 10))
axs = [ax1, ax2]
else:
fig, ax1 = plt.subplots(figsize=(6, 6))
ax2 = ax1
axs = [ax1]
plot_labels = parameter('plot_labels', [])
if plot_labels == []:
def test_J_integral(self):
"""
Check if the J-integral returns G=2*gamma
"""
if not atomistica:
print 'Atomistica not available. Skipping test.'
return
nx = 128
for calc, a0, C11, C12, C44, surface_energy, bulk_coordination in [
(atomistica.DoubleHarmonic(k1=1.0,
r1=1.0,
k2=1.0,
r2=math.sqrt(2),
cutoff=1.6),
clusters.sc('He', 1.0, [nx, nx, 1], [1, 0, 0],
[0, 1, 0]), 3, 1, 1, 0.05, 6),
# ( atomistica.Harmonic(k=1.0, r0=1.0, cutoff=1.3, shift=False),
# clusters.fcc('He', math.sqrt(2.0), [nx/2,nx/2,1], [1,0,0],
# [0,1,0]),
# math.sqrt(2), 1.0/math.sqrt(2), 1.0/math.sqrt(2), 0.05, 12)
]:
print '{} atoms.'.format(len(a0))
crack = CubicCrystalCrack(C11, C12, C44, [1, 0, 0], [0, 1, 0])
x, y, z = a0.positions.T
r2 = min(np.max(x) - np.min(x), np.max(y) - np.min(y)) / 4
r1 = r2 / 2
a = a0.copy()
a.center(vacuum=20.0, axis=0)
a.center(vacuum=20.0, axis=1)
ref = a.copy()
r0 = ref.positions
a.set_calculator(calc)
print 'epot = {}'.format(a.get_potential_energy())
sx, sy, sz = a.cell.diagonal()
tip_x = sx / 2
tip_y = sy / 2
k1g = crack.k1g(surface_energy)
g = a.get_array('groups')
old_x = tip_x + 1.0
old_y = tip_y + 1.0
while abs(tip_x - old_x) > 1e-6 and abs(tip_y - old_y) > 1e-6:
a.set_constraint(None)
ux, uy = crack.displacements(r0[:, 0], r0[:, 1], tip_x, tip_y,
k1g)
a.positions[:, 0] = r0[:, 0] + ux
a.positions[:, 1] = r0[:, 1] + uy
a.positions[:, 2] = r0[:, 2]
a.set_constraint(ase.constraints.FixAtoms(mask=g == 0))
opt = FIRE(a, logfile=None)
opt.run(fmax=1e-3)
old_x = tip_x
old_y = tip_y
tip_x, tip_y = crack.crack_tip_position(a.positions[:, 0],
a.positions[:, 1],
r0[:, 0],
r0[:, 1],
tip_x,
tip_y,
k1g,
mask=g != 0)
print tip_x, tip_y
# Get atomic strain
i, j = neighbour_list("ij", a, cutoff=1.3)
deformation_gradient, residual = \
atomic_strain(a, ref, neighbours=(i, j))
# Get atomic stresses
# Note: get_stresses returns the virial in Atomistica!
virial = a.get_stresses()
virial = Voigt_6_to_full_3x3_stress(virial)
# Compute J-integral
epot = a.get_potential_energies()
eref = np.zeros_like(epot)
for r1, r2 in [(r1, r2), (r1 / 2, r2 / 2), (r1 / 2, r2)]:
print 'r1 = {}, r2 = {}'.format(r1, r2)
J = J_integral(a, deformation_gradient, virial, epot, eref,
tip_x, tip_y, r1, r2)
print '2*gamma = {0}, J = {1}'.format(2 * surface_energy, J)
def test_J_integral(self):
"""
Check if the J-integral returns G=2*gamma
"""
if not atomistica:
print 'Atomistica not available. Skipping test.'
nx = 128
for calc, a0, C11, C12, C44, surface_energy, bulk_coordination in [
( atomistica.DoubleHarmonic(k1=1.0, r1=1.0, k2=1.0,
r2=math.sqrt(2), cutoff=1.6),
clusters.sc('He', 1.0, [nx,nx,1], [1,0,0], [0,1,0]),
3, 1, 1, 0.05, 6 ),
# ( atomistica.Harmonic(k=1.0, r0=1.0, cutoff=1.3, shift=False),
# clusters.fcc('He', math.sqrt(2.0), [nx/2,nx/2,1], [1,0,0],
# [0,1,0]),
# math.sqrt(2), 1.0/math.sqrt(2), 1.0/math.sqrt(2), 0.05, 12)
]:
print '{} atoms.'.format(len(a0))
crack = CubicCrystalCrack(C11, C12, C44, [1,0,0], [0,1,0])
x, y, z = a0.positions.T
r2 = min(np.max(x)-np.min(x), np.max(y)-np.min(y))/4
r1 = r2/2
a = a0.copy()
a.center(vacuum=20.0, axis=0)
a.center(vacuum=20.0, axis=1)
ref = a.copy()
r0 = ref.positions
a.set_calculator(calc)
print 'epot = {}'.format(a.get_potential_energy())
sx, sy, sz = a.cell.diagonal()
tip_x = sx/2
tip_y = sy/2
k1g = crack.k1g(surface_energy)
g = a.get_array('groups')
old_x = tip_x+1.0
old_y = tip_y+1.0
while abs(tip_x-old_x) > 1e-6 and abs(tip_y-old_y) > 1e-6:
a.set_constraint(None)
ux, uy = crack.displacements(r0[:,0], r0[:,1], tip_x, tip_y,
k1g)
a.positions[:,0] = r0[:,0] + ux
a.positions[:,1] = r0[:,1] + uy
a.positions[:,2] = r0[:,2]
a.set_constraint(ase.constraints.FixAtoms(mask=g==0))
opt = FIRE(a, logfile=None)
opt.run(fmax=1e-3)
old_x = tip_x
old_y = tip_y
tip_x, tip_y = crack.crack_tip_position(a.positions[:,0],
a.positions[:,1],
r0[:,0], r0[:,1],
tip_x, tip_y, k1g,
mask=g!=0)
print tip_x, tip_y
# Get atomic strain
i, j = neighbour_list("ij", a, cutoff=1.3)
deformation_gradient, residual = \
atomic_strain(a, ref, neighbours=(i, j))
# Get atomic stresses
# Note: get_stresses returns the virial in Atomistica!
virial = a.get_stresses()
virial = Voigt_6_to_full_3x3_stress(virial)
# Compute J-integral
epot = a.get_potential_energies()
eref = np.zeros_like(epot)
for r1, r2 in [(r1, r2), (r1/2, r2/2), (r1/2, r2)]:
print 'r1 = {}, r2 = {}'.format(r1, r2)
J = J_integral(a, deformation_gradient, virial, epot, eref,
tip_x, tip_y, r1, r2)
print '2*gamma = {0}, J = {1}'.format(2*surface_energy, J)
def test_J_integral(self):
if quadrature is None:
print('No scipy.integrate.quadrature. Skipping J-integral test.')
return
for C11, C12, C44, surface_energy, k1 in self.materials:
crack = CubicCrystalCrack([1,0,0], [0,1,0], C11, C12, C44)
k = crack.k1g(surface_energy)*k1
def polar_path(theta, r=1, x0=0, y0=0):
nx = np.cos(theta)
ny = np.sin(theta)
n = np.transpose([nx, ny])
return r*n-np.array([x0, y0]), n, r
def elliptic_path(theta, r=1, x0=0, y0=0):
rx, ry = r
x = rx*np.cos(theta)
y = ry*np.sin(theta)
nx = ry*np.cos(theta)
ny = rx*np.sin(theta)
ln = np.sqrt(nx**2+ny**2)
nx /= ln
ny /= ln
ds = np.sqrt((rx*np.sin(theta))**2 + (ry*np.cos(theta))**2)
return np.transpose([x-x0, y-y0]), np.transpose([nx, ny]), ds
def rectangular_path(t, r):
x = -r*np.ones_like(t)
y = r*(t-8)
nx = -np.ones_like(t)
ny = np.zeros_like(t)
x = np.where(t < 7, r*(6-t), x)
y = np.where(t < 7, -r*np.ones_like(t), y)
nx = np.where(t < 7, np.zeros_like(t), nx)
ny = np.where(t < 7, -np.ones_like(t), ny)
x = np.where(t < 5, r*np.ones_like(t), x)
y = np.where(t < 5, r*(4-t), y)
nx = np.where(t < 5, np.ones_like(t), nx)
ny = np.where(t < 5, np.zeros_like(t), ny)
x = np.where(t < 3, r*(t-2), x)
y = np.where(t < 3, r*np.ones_like(t), y)
nx = np.where(t < 3, np.zeros_like(t), nx)
ny = np.where(t < 3, np.ones_like(t), ny)
x = np.where(t < 1, -r*np.ones_like(t), x)
y = np.where(t < 1, r*t, y)
nx = np.where(t < 1, -np.ones_like(t), nx)
ny = np.where(t < 1, np.zeros_like(t), ny)
return np.transpose([x, y]), np.transpose([nx, ny]), r
def J(t, path_func=polar_path):
# Position, normal to path, length
pos, n, ds = path_func(t)
x, y = pos.T
nx, ny = n.T
# Stress tensor
sxx, syy, sxy = crack.stresses(x, y, 0, 0, k)
s = np.array([[sxx, sxy], [sxy, syy]]).T
# Deformation gradient and strain tensor
F = crack.deformation_gradient(x, y, 0, 0, k)
eps = (F+F.swapaxes(1, 2))/2 - np.identity(2).reshape(1, 2, 2)
# Strain energy density
W = (s*eps).sum(axis=2).sum(axis=1)/2
# Note dy == nx*ds
retval = (W*nx - np.einsum('...j,...jk,...k->...', n, s, F[..., 0, :]))*ds
return retval
eps = 1e-6
for r in [1, 10, 100]:
# Polar path
J_val, J_err = quadrature(J, -np.pi+eps, np.pi-eps,
args=(lambda t: polar_path(t, r)), )
self.assertAlmostEqual(J_val, 2*surface_energy, places=2)
# Elliptic path
J_val, J_err = quadrature(J, -np.pi+eps, np.pi-eps,
args=(lambda t: elliptic_path(t, (3*r, r)), ),
maxiter=200)
self.assertAlmostEqual(J_val, 2*surface_energy, places=2)
# Elliptic path, shifted in x and y directions off-center
J_val, J_err = quadrature(J, -np.pi+eps, np.pi-eps,
args=(lambda t: elliptic_path(t, (r, 1.5*r), 0, 0.5), ),
maxiter=200)
self.assertAlmostEqual(J_val, 2*surface_energy, places=2)