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)
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)
f_dimer = np.array(f_dimer)
f_num = np.array(f_num)
assert abs(f_dimer - f_num).max() < 0.1
crystal = triangular_lattice_slab(params.a, 3*params.N, params.N)
calc.set_reference_crystal(crystal)
crystal.set_calculator(calc)
e0 = crystal.get_potential_energy()
l = crystal.cell[0,0]
h = crystal.cell[1,1]
print 'l=', l, 'h=', h
# compute surface (Griffith) energy
b = crystal.copy()
b.set_calculator(calc)
shift = calc.parameters['rc']*2
y = crystal.positions[:, 1]
b.positions[y > h/2, 1] += shift
b.cell[1, 1] += shift
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)
f_dimer = np.array(f_dimer)
f_num = np.array(f_num)
assert abs(f_dimer - f_num).max() < 0.1
crystal = triangular_lattice_slab(params.a, 3*params.N, params.N)
calc.set_reference_crystal(crystal)
crystal.set_calculator(calc)
e0 = crystal.get_potential_energy()
l = crystal.cell[0,0]
h = crystal.cell[1,1]
print 'l=', l, 'h=', h
# compute surface (Griffith) energy
b = crystal.copy()
b.set_calculator(calc)
shift = calc.parameters['rc']*2
y = crystal.positions[:, 1]
b.positions[y > h/2, 1] += shift
b.cell[1, 1] += shift
def test_neighbour_list_triangular(self):
a = triangular_lattice_slab(1.0, 2, 2)
i, j, D, S = neighbour_list('ijDS', a, 1.2)
D2 = a.positions[j] - a.positions[i] + S.dot(a.cell)
self.assertArrayAlmostEqual(D, D2)
def test_new_style_interface(self):
calc = IdealBrittleSolid()
atoms = triangular_lattice_slab(1.0, 5, 5)
self.rattle_calc(atoms, calc)
def test_neighbour_list_triangular(self):
a = triangular_lattice_slab(1.0, 2, 2)
i, j, D, S = neighbour_list('ijDS', a, 1.2)
D2 = a.positions[j] - a.positions[i] + S.dot(a.cell)
self.assertArrayAlmostEqual(D, D2)