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)