quip_client = QUIPClient(client_id=0,
exe=os.path.join(os.environ['QUIP_ROOT'],
'build.' + os.environ['QUIP_ARCH'],
'socktest'),
param_files=['params.xml'],
env=os.environ)
sock_calc = SocketCalculator(quip_client)
el = 'Si'
a0 = 5.43
n = [6, 4, 1]
crack_surface = [1, 1, 1]
crack_front = [1, -1, 0]
cryst = diamond(el, a0, n, crack_surface, crack_front)
cryst.pbc = [True, True, True] # QUIP doesn't handle open BCs
cryst.rattle(0.01)
cryst.set_calculator(sock_calc)
sock_e = cryst.get_potential_energy()
sock_f = cryst.get_forces()
sock_s = cryst.get_stress()
sock_calc.shutdown()
# compare to results from quippy
quippy_calc = Potential('IP SW', param_filename='params.xml')
cryst.set_calculator(quippy_calc)
quippy_e = cryst.get_potential_energy()
quippy_f = cryst.get_forces()
quippy_s = cryst.get_stress()
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
surface_energy = 1.08 * 10 # GPa*A = 0.1 J/m^2
# Crack system
n = [ 4, 6, 1 ]
crack_surface = [ 1,-1, 0 ]
crack_front = [ 1, 1, 0 ]
crack_tip = [ 41, 56 ]
skin_x, skin_y = 1, 1
vacuum = 6.0
# Simulation control
nsteps = 31
# Increase stress intensity factor
k1 = np.linspace(0.8, 1.5, nsteps)
# Don't move crack tip
tip_dx = np.zeros_like(k1)
tip_dz = np.zeros_like(k1)
fmax = 0.05
# Setup crack system
cryst = diamond(el, a0, n, crack_surface, crack_front)
set_groups(cryst, n, skin_x, skin_y)
ase.io.write('cryst.cfg', cryst)
# Compute crack tip position
r0 = np.sum(cryst.get_positions()[crack_tip,:], axis=0)/len(crack_tip)
tip_x0, tip_y0, tip_z0 = r0
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