def diamond_110_001(el, a0, n, crack_surface=[1,1,0], crack_front=[0,0,1],
skin_x=1.0, skin_y=1.0, vac=5.0):
nx, ny, nz = n
third_dir = np.cross(crack_surface, crack_front)
directions = [ third_dir, crack_surface, crack_front ]
if np.linalg.det(directions) < 0:
third_dir = -third_dir
directions = [ third_dir, crack_surface, crack_front ]
a = Diamond(el, latticeconstant = a0, size = [ nx,ny,nz ],
directions = directions)
sx, sy, sz = a.get_cell().diagonal()
a.translate([a0/100,a0/100,a0/100])
a.set_scaled_positions(a.get_scaled_positions())
a.center()
lx = skin_x*sx/nx
ly = skin_y*sy/ny
r = a.get_positions()
g = np.where(
np.logical_or(
np.logical_or(
np.logical_or(
r[:, 0] < lx, r[:, 0] > sx-lx),
r[:, 1] < ly),
r[:, 1] > sy-ly),
np.zeros(len(a), dtype=int),
np.ones(len(a), dtype=int))
a.set_array('groups', g)
a.set_cell([sx+2*vac, sy+2*vac, sz])
a.translate([vac, vac, 0.0])
a.set_pbc([False, False, True])
return a
def dia_100_2x1(sym, a0):
sym = string2symbols(sym)
if len(sym) == 1:
a = Diamond(sym[0],
size = [2*nx, nx, nz],
latticeconstant = a0,
directions=[ [1,-1,0], [1,1,0], [0,0,1] ]
)
else:
a = B3(sym,
size = [2*nx, nx, nz],
latticeconstant = a0,
directions=[ [1,-1,0], [1,1,0], [0,0,1] ]
)
sx, sy, sz = a.get_cell().diagonal()
a.translate([sx/(8*nx), sy/(8*nx), sz/(8*nz)])
bulk = a.copy()
for i in a:
if i.z < sz/(4*nz) or i.z > sz-sz/(4*nz):
if i.x < sx/2:
i.x = i.x+0.5
else:
i.x = i.x-0.5
return bulk, a
def dia_111(sym, a0):
sym = string2symbols(sym)
if len(sym) == 1:
a = Diamond(sym[0],
size=[nx, nx, nz],
latticeconstant=a0,
directions=[[1, -1, 0], [1, 1, -2], [1, 1, 1]])
else:
a = B3(sym,
size=[nx, nx, nz],
latticeconstant=a0,
directions=[[1, -1, 0], [1, 1, -2], [1, 1, 1]])
sx, sy, sz = a.get_cell().diagonal()
a.translate([sx / (12 * nx), sy / (4 * nx), sz / (12 * nz)])
return a
def dia_111_pandey(sym, a0, nx=nx, ny=nx, nz=nz):
"""2x1 Pandey reconstructed (111) surface."""
sym = string2symbols(sym)
if len(sym) == 1:
a = Diamond(sym[0],
size = [nx, ny, nz],
latticeconstant = a0,
directions=[ [1,-1,0], [1,1,-2], [1,1,1] ]
)
else:
a = B3(sym,
size = [nx, ny, nz],
latticeconstant = a0,
directions=[ [1,-1,0], [1,1,-2], [1,1,1] ]
)
sx, sy, sz = a.get_cell().diagonal()
a.translate([sx/(12*nx), sy/(4*ny), sz/(6*nz)])
a.set_scaled_positions(a.get_scaled_positions()%1.0)
bulk = a.copy()
bondlen = a0*sqrt(3)/4
x, y, z = a.positions.T
mask = np.abs(z-z.max()) < 0.1*a0
top1, top2 = np.arange(len(a))[mask].reshape(-1, 2).T
mask = np.logical_and(np.abs(z-z.max()) < bondlen, np.logical_not(mask))
topA, topB = np.arange(len(a))[mask].reshape(-1, 2).T
y[topA] += bondlen/3
y[topB] -= bondlen/3
y[top1] += bondlen
x[top1] += a.cell[0,0]/(2*nx)
x[top2] += a.cell[0,0]/(2*nx)
mask = np.abs(z-z.min()) < 0.1*a0
bot1, bot2 = np.arange(len(a))[mask].reshape(-1, 2).T
mask = np.logical_and(np.abs(z-z.min()) < bondlen, np.logical_not(mask))
botA, botB = np.arange(len(a))[mask].reshape(-1, 2).T
y[botA] += bondlen/3
y[botB] -= bondlen/3
y[bot2] -= bondlen
x[bot2] += a.cell[0,0]/(2*nx)
x[bot1] += a.cell[0,0]/(2*nx)
a.set_scaled_positions(a.get_scaled_positions()%1.0)
return bulk, a
def dia_111(sym, a0):
sym = string2symbols(sym)
if len(sym) == 1:
a = Diamond(sym[0],
size = [nx, nx, nz],
latticeconstant = a0,
directions=[ [1,-1,0], [1,1,-2], [1,1,1] ]
)
else:
a = B3(sym,
size = [nx, nx, nz],
latticeconstant = a0,
directions=[ [1,-1,0], [1,1,-2], [1,1,1] ]
)
sx, sy, sz = a.get_cell().diagonal()
a.translate([sx/(12*nx), sy/(4*nx), sz/(12*nz)])
return a
def diamond_110_110(el, a0, n, crack_surface=[1,1,0],
crack_front=[1,-1,0],
skin_x=0.5, skin_y=1.0,
central_x=-1.0, central_y=-1.0,
vac=5.0):
nx, ny, nz = n
third_dir = np.cross(crack_surface, crack_front)
a = Diamond(el,
latticeconstant = a0,
size = [nx, ny, nz],
directions = [third_dir, crack_surface, crack_front]
)
sx, sy, sz = a.get_cell().diagonal()
a.translate([sx/(8*nx), sy/(4*ny), sz/(4*nz)])
a.set_scaled_positions(a.get_scaled_positions())
skin_x = skin_x*sx/nx
skin_y = skin_y*sy/ny
r = a.get_positions()
g = np.where(
np.logical_or(
np.logical_or(
np.logical_or(
r[:, 0] < skin_x, r[:, 0] > sx-skin_x),
r[:, 1] < skin_y),
r[:, 1] > sy-skin_y),
np.zeros(len(a), dtype=int),
np.ones(len(a), dtype=int))
g = np.where(
np.logical_or(
np.logical_or(
np.logical_or(
r[:, 0] < sx/2-central_x, r[:, 0] > sx/2+central_x),
r[:, 1] < sy/2-central_y),
r[:, 1] > sy/2+central_y),
g,
2*np.ones(len(a), dtype=int))
a.set_array('groups', g)
a.set_cell([sx+2*vac, sy+2*vac, sz])
a.translate([vac, vac, 0.0])
a.set_pbc([False, False, True])
return a
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_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)
# set of utility routines specific this this model/testing framework from utilities import relax_atoms, relax_atoms_cell # the current model import model a0 = 5.44 # initial guess at lattice constant, cell will be relaxed below fmax = 0.01 # maximum force following relaxtion [eV/A] # set up the a bulk = Diamond(symbol='Si', latticeconstant=a0, directions=[[1,-1,0],[0,0,1],[1,1,0]]) # specify that we will use model.calculator to compute forces, energies and stresses bulk.set_calculator(model.calculator) # flip coord system for ASE (precon minim?) c = bulk.get_cell() t_v = c[0,:].copy() c[0,:] = c[1,:] c[1,:] = t_v bulk.set_cell(c) # use one of the routines from utilities module to relax the initial # unit cell and atomic positions bulk = relax_atoms_cell(bulk, tol=fmax, traj_file=None) # set up supercell bulk *= (1, 1, 5) ase.io.write(sys.stdout, bulk, format='extxyz') def surface_energy(bulk, z_offset, opening):
fmax = 0.01 # maximum force following relaxtion [eV/A]
if not hasattr(model, 'bulk_reference'):
print("Did not find bulk_reference, recalculating bulk")
# set up the a
bulk = Diamond(symbol='Si', latticeconstant=a0)
# specify that we will use model.calculator to compute forces, energies and stresses
bulk.set_calculator(model.calculator)
# use one of the routines from utilities module to relax the initial
# unit cell and atomic positions
bulk = relax_atoms_cell(bulk, tol=fmax, traj_file=None)
else:
bulk = model.bulk_reference.copy()
print("Found bulk_reference, lattice constant", bulk.get_cell()[0,0] )
bulk.set_calculator(model.bulk_reference.calc)
a0 = bulk.cell[0,0] # get lattice constant from relaxed bulk
e0 = bulk.get_potential_energy()/8.0
print "got a0 ", a0
print "got e0 ", e0
def defect_energy(a0, e0, filename):
tmp = ase.io.read(os.path.dirname(__file__)+"/"+filename, index=':', format='extxyz')
defect = tmp[0]
# adjust lattice constant
