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
###
sx = 2
dx = 1e-6
dev_thres = 1e-4
###
tests = [
( r6, dict(el1='Si', el2='Si', A=1.0, r0=1.0, cutoff=5.0),
[ ( "dia-Si", Diamond("Si", size=[sx,sx,sx]) ) ] ),
( Brenner, Erhart_PRB_71_035211_SiC,
[ ( "dia-C", Diamond("C", size=[sx,sx,sx]) ),
( "dia-Si", Diamond("Si", size=[sx,sx,sx]) ),
( "dia-Si-C", B3( [ "Si", "C" ], latticeconstant=4.3596,
size=[sx,sx,sx]) ) ] ),
( BrennerScr, Erhart_PRB_71_035211_SiC__Scr,
[ ( "dia-C", Diamond("C", size=[sx,sx,sx]) ),
( "dia-Si", Diamond("Si", size=[sx,sx,sx]) ),
( "dia-Si-C", B3( [ "Si", "C" ], latticeconstant=4.3596,
size=[sx,sx,sx]) ) ] ),
( Brenner, Henriksson_PRB_79_114107_FeC,
[ dict( name='dia-C', struct=Diamond('C', size=[sx,sx,sx]) ),
dict( name='bcc-Fe',
struct=BodyCenteredCubic('Fe', size=[sx,sx,sx]) ),
dict( name='fcc-Fe',
struct=FaceCenteredCubic('Fe', size=[sx,sx,sx],
latticeconstant=3.6) ),
dict( name='sc-Fe',
struct=SimpleCubic('Fe', size=[sx,sx,sx], latticeconstant=2.4) ),
dict( name='B1-Fe-C',
[ ( "dia-C", Diamond("C", size=[sx,sx,sx]),
# Ec a0 C11 C12 C44 B Cp
None, None, None, None, None, None, None ),
] ),
( Brenner, Brenner_PRB_42_9458_C_II,
[ ( "dia-C", Diamond("C", size=[sx,sx,sx]),
# Ec a0 C11 C12 C44 B Cp
7.376-0.0524, 3.558, 621, 415, 383, 484, None ),
] ),
( Brenner, Erhart_PRB_71_035211_SiC,
[ ( "dia-C", Diamond("C", size=[sx,sx,sx]),
# Ec a0 C11 C12 C44 B Cp
7.3731, 3.566, 1082, 127, 673, 445, None ),
dict( name="dia-Si", struct=Diamond("Si", size=[sx,sx,sx]),
Ec=4.63, a0=5.429, C11=167, C12=65, C440=105, B=99 ),
dict( name="dia-Si-C", struct=B3( [ "Si", "C" ], latticeconstant=4.3596,
size=[sx,sx,sx]),
Ec=6.340,a0=4.359, C11=382, C12=145, C440=305, B=224 ) ] ),
( BrennerScr, Erhart_PRB_71_035211_SiC__Scr,
[ ( "dia-C", Diamond("C", size=[sx,sx,sx]),
# Ec a0 C11 C12 C44 B Cp
7.3731, 3.566, 1082, 127, 673, 445, None ),
dict( name="dia-Si", struct=Diamond("Si", size=[sx,sx,sx]),
Ec=4.63, a0=5.429, C11=167, C12=65, C440=105, B=99 ),
dict( name="dia-Si-C", struct=B3( [ "Si", "C" ], latticeconstant=4.3596,
size=[sx,sx,sx]),
Ec=6.340,a0=4.359, C11=382, C12=145, C440=305, B=224 ) ] ),
( Kumagai, Kumagai_CompMaterSci_39_457_Si,
[ dict( name="dia-Si", struct=Diamond("Si", size=[sx,sx,sx]),
Ec=4.630, a0=5.429, C11=166.4, C12=65.3, C440=120.9 ),
] ),
( KumagaiScr, Kumagai_CompMaterSci_39_457_Si__Scr,
1082,
127,
673,
445,
None),
dict(name="dia-Si",
struct=Diamond("Si", size=[sx, sx, sx]),
Ec=4.63,
a0=5.429,
C11=167,
C12=65,
C440=105,
B=99),
dict(name="dia-Si-C",
struct=B3(["Si", "C"],
latticeconstant=4.3596,
size=[sx, sx, sx]),
Ec=6.340,
a0=4.359,
C11=382,
C12=145,
C440=305,
B=224)
]),
(
BrennerScr,
Erhart_PRB_71_035211_SiC__Scr,
[
(
"dia-C",
Diamond("C", size=[sx, sx, sx]),