def test_forces_linear(self):
a = triangular_lattice_slab(1.0, 1, 1)
calc = IdealBrittleSolid(rc=1.2, beta=0.0, linear=True)
calc.set_reference_crystal(a)
a.set_calculator(calc)
a.rattle(0.01)
f = a.get_forces()
fn = calc.calculate_numerical_forces(a)
self.assertArrayAlmostEqual(f, fn, tol=self.tol)
def test_forces_and_virial(self):
a = triangular_lattice_slab(1.0, 2, 2)
calc = IdealBrittleSolid(rc=1.2, beta=0.0)
a.set_calculator(calc)
a.rattle(0.1)
f = a.get_forces()
fn = calc.calculate_numerical_forces(a)
self.assertArrayAlmostEqual(f, fn, tol=self.tol)
self.assertArrayAlmostEqual(a.get_stress(),
calc.calculate_numerical_stress(a),
tol=self.tol)
def test_anisotropic_near_field_solution(self):
"""
Run an atomistic calculation of a harmonic solid and compare to
continuum solution.
"""
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),
IdealBrittleSolid(k=1.0, a=1.0, rc=1.3),
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', write_results=False)
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
i = neighbour_list("i", a, 1.1)
coord = np.bincount(i, minlength=len(a))
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)
from ase.md import VelocityVerlet
from ase.optimize.fire import FIRE
from matscipy.fracture_mechanics.idealbrittlesolid import (IdealBrittleSolid,
triangular_lattice_slab,
find_crack_tip,
set_initial_velocities,
set_constraints,
extend_strip)
from matscipy.fracture_mechanics.crack import thin_strip_displacement_y
sys.path.insert(0, '.')
import params
calc = IdealBrittleSolid(rc=params.rc, k=params.k, a=params.a, beta=params.beta)
x_dimer = np.linspace(params.a-(params.rc-params.a),
params.a+1.1*(params.rc-params.a),51)
dimers = [Atoms('Si2', [(0, 0, 0), (x, 0, 0)],
cell=[10., 10., 10.], pbc=True) for x in x_dimer]
calc.set_reference_crystal(dimers[0])
e_dimer = []
f_dimer = []
f_num = []
for d in dimers:
d.set_calculator(calc)
e_dimer.append(d.get_potential_energy())
f_dimer.append(d.get_forces())
f_num.append(calc.calculate_numerical_forces(d))
e_dimer = np.array(e_dimer)
from ase.optimize.fire import FIRE
from matscipy.fracture_mechanics.idealbrittlesolid import (IdealBrittleSolid,
triangular_lattice_slab,
find_crack_tip,
set_initial_velocities,
set_constraints,
extend_strip)
from matscipy.fracture_mechanics.crack import (thin_strip_displacement_y,
ConstantStrainRate)
sys.path.insert(0, '.')
import params
calc = IdealBrittleSolid(rc=params.rc, k=params.k, a=params.a, beta=params.beta)
x_dimer = np.linspace(params.a-(params.rc-params.a),
params.a+1.1*(params.rc-params.a),51)
dimers = [Atoms('Si2', [(0, 0, 0), (x, 0, 0)],
cell=[10., 10., 10.], pbc=True) for x in x_dimer]
calc.set_reference_crystal(dimers[0])
e_dimer = []
f_dimer = []
f_num = []
for d in dimers:
d.set_calculator(calc)
e_dimer.append(d.get_potential_energy())
f_dimer.append(d.get_forces())
f_num.append(calc.calculate_numerical_forces(d))
e_dimer = np.array(e_dimer)