def test_no_pbc_small_cell(self):
a = io.read('aC.cfg')
a.set_calculator(Tersoff())
a.set_pbc(False)
e1 = a.get_potential_energy()
i1, j1, r1 = a.calc.nl.get_neighbors(a.calc.particles)
a.set_cell(a.cell*0.9, scale_atoms=False)
e2 = a.get_potential_energy()
self.assertAlmostEqual(e1, e2)
i2, j2, r2 = a.calc.nl.get_neighbors(a.calc.particles)
for k in range(len(a)):
neigh1 = np.array(sorted(j1[i1==k]))
neigh2 = np.array(sorted(j2[i2==k]))
self.assertTrue(np.all(neigh1 == neigh2))
def test_pbc_shift_by_multiple_cells(self):
a = io.read('aC.cfg')
a.set_calculator(Tersoff())
e1 = a.get_potential_energy()
i1, j1, r1 = a.calc.nl.get_neighbors(a.calc.particles)
a[100].position += 3*a.cell[0]
e2 = a.get_potential_energy()
i2, j2, r2 = a.calc.nl.get_neighbors(a.calc.particles)
for i in range(len(a)):
n1 = np.array(sorted(j1[i1==i]))
n2 = np.array(sorted(j2[i2==i]))
if np.any(n1 != n2):
print(i, n1, n2)
a[100].position += a.cell.T.dot([1,3,-4])
e3 = a.get_potential_energy()
self.assertAlmostEqual(e1, e2)
self.assertAlmostEqual(e1, e3)
def test_pbc(self):
a = Diamond('Si', latticeconstant=5.432, size=[2,2,2])
sx, sy, sz = a.get_cell().diagonal()
a.set_calculator(Tersoff())
e1 = a.get_potential_energy()
a.set_pbc([True,True,False])
e2 = a.get_potential_energy()
a.set_pbc(True)
a.set_cell([sx,sy,2*sz])
e3 = a.get_potential_energy()
self.assertEqual(e2, e3)
# This should give the unrelaxed surface energy
esurf = (e2-e1)/(2*sx*sy) * Jm2
self.assertTrue(abs(esurf-2.309) < 0.001)
def test_floating_point_issue(self):
calc = Tersoff()
a1 = ase.Atoms('Si4C4', positions=np.array([[-4.41173839e-52, 0.00000000e+00, 0.00000000e+00],
[-4.41173839e-52, 2.26371743e+00, 2.26371743e+00],
[ 2.26371743e+00, 0.00000000e+00, 2.26371743e+00],
[ 2.26371743e+00, 2.26371743e+00, 0.00000000e+00],
[ 1.13185872e+00, 1.13185872e+00, 1.13185872e+00],
[ 1.13185872e+00, 3.39557615e+00, 3.39557615e+00],
[ 3.39557615e+00, 1.13185872e+00, 3.39557615e+00],
[ 3.39557615e+00, 3.39557615e+00, 1.13185872e+00]]),
cell=[4.527434867899659, 4.527434867899659, 4.527434867899659], pbc=True)
a1.calc = calc
a1.get_potential_energy()
self.assertTrue((calc.nl.get_coordination_numbers(calc.particles, 3.0) == 4).all())
a2 = a1.copy()
a2.calc = calc
a2.set_scaled_positions(a2.get_scaled_positions())
a2.get_potential_energy()
self.assertTrue((calc.nl.get_coordination_numbers(calc.particles, 3.0) == 4).all())
def test_mask_decomposition_bop(self):
a = io.read('aC.cfg')
for pot in [Tersoff, TersoffScr]:
c = Tersoff()
a.set_calculator(c)
self.random_mask_test(a)
from ase.optimize import FIRE, LBFGS, LBFGSLineSearch
from ase.optimize.precon import PreconLBFGS
from ase.build import bulk
from atomistica import Tersoff
from ode import ODE12rOptimizer
a0 = bulk('C', cubic=True) * 5
a0.rattle(0.05)
del a0[0]
for OPT in [ODE12rOptimizer, FIRE, LBFGS, LBFGSLineSearch, PreconLBFGS]:
a = a0.copy()
a.set_calculator(Tersoff())
opt = OPT(a)
opt.run(fmax=1e-3)
print()
def test_embedding_size_convergence(self):
calc = Tersoff(**Tersoff_PRB_39_5566_Si_C)
el = 'C'
a0 = 3.566
surface_energy = 2.7326 * 10
crack_surface = [1, 1, 1]
crack_front = [1, -1, 0]
skin_x, skin_y = 1, 1
cryst = bulk(el, cubic=True)
cryst.set_calculator(calc)
FIRE(UnitCellFilter(cryst), logfile=None).run(fmax=1e-6)
a0 = cryst.cell.diagonal().mean()
bondlength = cryst.get_distance(0, 1)
#print('a0 =', a0, ', bondlength =', bondlength)
cryst = diamond(el, a0, [1, 1, 1], crack_surface, crack_front)
cryst.set_pbc(True)
cryst.set_calculator(calc)
cryst.set_cell(cryst.cell.diagonal(), scale_atoms=True)
C, C_err = fit_elastic_constants(cryst,
verbose=False,
symmetry='cubic',
optimizer=FIRE,
fmax=1e-6)
#print('Measured elastic constants (in GPa):')
#print(np.round(C*10/units.GPa)/10)
bondlengths = []
refcell = None
reftip_x = None
reftip_y = None
#[41, 39, 1],
for i, n in enumerate([[21, 19, 1], [11, 9, 1], [6, 5, 1]]):
#print(n)
cryst = diamond(el, a0, n, crack_surface, crack_front)
set_groups(cryst, n, skin_x, skin_y)
cryst.set_pbc(True)
cryst.set_calculator(calc)
FIRE(UnitCellFilter(cryst), logfile=None).run(fmax=1e-6)
cryst.set_cell(cryst.cell.diagonal(), scale_atoms=True)
ase.io.write('cryst_{}.xyz'.format(i), cryst, format='extxyz')
crk = crack.CubicCrystalCrack(crack_surface,
crack_front,
Crot=C / units.GPa)
k1g = crk.k1g(surface_energy)
tip_x = cryst.cell.diagonal()[0] / 2
tip_y = cryst.cell.diagonal()[1] / 2
a = cryst.copy()
a.set_pbc([False, False, True])
k1 = 1.0
ux, uy = crk.displacements(cryst.positions[:, 0],
cryst.positions[:, 1], tip_x, tip_y,
k1 * k1g)
a.positions[:, 0] += ux
a.positions[:, 1] += uy
# Center notched configuration in simulation cell and ensure enough vacuum.
oldr = a[0].position.copy()
if refcell is None:
a.center(vacuum=10.0, axis=0)
a.center(vacuum=10.0, axis=1)
refcell = a.cell.copy()
tip_x += a[0].x - oldr[0]
tip_y += a[0].y - oldr[1]
reftip_x = tip_x
reftip_y = tip_y
else:
a.set_cell(refcell)
# Shift tip position so all systems are exactly centered at the same spot
a.positions[:, 0] += reftip_x - tip_x
a.positions[:, 1] += reftip_y - tip_y
refpositions = a.positions.copy()
# Move reference crystal by same amount
cryst.set_cell(a.cell)
cryst.set_pbc([False, False, True])
cryst.translate(a[0].position - oldr)
bond1, bond2 = crack.find_tip_coordination(
a, bondlength=bondlength * 1.2)
# Groups mark the fixed region and the region use for fitting the crack tip.
g = a.get_array('groups')
gcryst = cryst.get_array('groups')
ase.io.write('cryst_{}.xyz'.format(i), cryst)
a.set_calculator(calc)
a.set_constraint(FixAtoms(mask=g == 0))
FIRE(a, logfile=None).run(fmax=1e-6)
dpos = np.sqrt((
(a.positions[:, 0] - refpositions[:, 0]) / ux)**2 + (
(a.positions[:, 1] - refpositions[:, 1]) / uy)**2)
a.set_array('dpos', dpos)
distance_from_tip = np.sqrt((a.positions[:, 0] - reftip_x)**2 +
(a.positions[:, 1] - reftip_y)**2)
ase.io.write('crack_{}.xyz'.format(i), a)
# Compute average bond length per atom
neighi, neighj, neighd = neighbour_list('ijd',
a,
cutoff=bondlength *
1.2)
coord = np.bincount(neighi)
assert coord.max() == 4
np.savetxt(
'dpos_{}.out'.format(i),
np.transpose(
[distance_from_tip[coord == 4], dpos[coord == 4]]))
# Compute distances from tipcenter
neighdist = np.sqrt((
(a.positions[neighi, 0] + a.positions[neighj, 0]) / 2 -
reftip_x)**2 + (
(a.positions[neighi, 1] + a.positions[neighj, 1]) / 2 -
reftip_y)**2)
np.savetxt('bl_{}.out'.format(i),
np.transpose([neighdist, neighd]))
bondlengths += [a.get_distance(bond1, bond2)]
print(bondlengths, np.diff(bondlengths),
bondlengths / bondlengths[-1] - 1)
assert np.all(np.diff(bondlengths) > 0)
assert np.max(bondlengths / bondlengths[0] - 1) < 0.01
from atomistica import Tersoff, Tersoff_PRB_39_5566_Si_C # A module defining a module needs to define only one variable, # named `calculator`, which should be an instance of the ase.calculator.Calculator, # a subclass of this, or a compatible class implementing the calculator interface. calculator = Tersoff(**Tersoff_PRB_39_5566_Si_C) no_checkpoint = True name = 'Tersoff'
