def nanotube_data(n, m, R=1.42):
"""
Return a dictionary if miscellaneous nanotube data
"""
from hotbit import Atoms
a = sqrt(3.0) * R
data = {}
data['a'] = a
data['diameter'] = a / pi * sqrt(n**2 + m**2 + n * m)
data['radius'] = data['diameter'] / 2
data['C'] = data['diameter'] * pi
if n == m:
d = n
dR = 3 * n
else:
d = gcd(n, m)
if np.mod(n - m, 3 * d) == 0:
dR = 3 * d
else:
dR = d
data['T'] = 3 * R * sqrt(n**2 + m**2 + n * m) / dR
data['metallic'] = (np.mod(n - m, 3) == 0)
data['semiconducting'] = not data['metallic']
data['angle'] = atan(sqrt(3) * m / (m + 2 * n))
data['hexagons_per_cell'] = int(round(2 * (m**2 + n**2 + m * n) / dR, 0))
if n == m:
data['type'] = 'armchair'
elif n == 0 or m == 0:
data['type'] = 'zigzag'
else:
data['type'] = 'chiral'
return data
def nanotube_data(n,m,R=1.42):
"""
Return a dictionary if miscellaneous nanotube data
"""
from hotbit import Atoms
a=sqrt(3.0)*R
data={}
data['a'] = a
data['diameter'] = a/pi*sqrt(n**2+m**2+n*m)
data['radius'] = data['diameter']/2
data['C'] = data['diameter']*pi
if n==m:
d = n
dR = 3*n
else:
d = gcd(n,m)
if np.mod(n-m,3*d)==0:
dR = 3*d
else:
dR = d
data['T'] = 3*R*sqrt(n**2+m**2+n*m)/dR
data['metallic'] = (np.mod(n-m,3)==0)
data['semiconducting'] = not data['metallic']
data['angle'] = atan( sqrt(3)*m/(m+2*n) )
data['hexagons_per_cell'] = int(round(2*(m**2+n**2+m*n)/dR,0))
if n==m:
data['type'] = 'armchair'
elif n==0 or m==0:
data['type'] = 'zigzag'
else:
data['type'] = 'chiral'
return data
def nanotube(n, m, R=1.42, length=1, element='C'):
'''
Create a nanotube around z-axis.
parameters:
-----------
n,m: chiral indices
R: nearest neighbor distance
length: number of unit cells
element: element symbol
'''
from hotbit import Atoms
at = Atoms(pbc=(False, False, True))
sq3 = sqrt(3.0)
a0 = R
gcn = gcd(n, m)
a1 = np.array([sq3 / 2, 0.5]) * a0 * sq3
a2 = np.array([sq3 / 2, -0.5]) * a0 * sq3
h = float(float(n) - float(m)) / float(3 * gcn)
if h - int(h) == 0.0:
RR = 3
else:
RR = 1
c = n * a1 + m * a2
abs_c = sqrt(dot(c, c))
a = (-(2 * m + n) * a1 + (2 * n + m) * a2) / (gcn * RR)
abs_a = sqrt(dot(a, a))
eps = 0.01
b = [[1. / 3 - eps, 1. / 3 - eps], [2. / 3 - eps, 2. / 3 - eps]]
nxy = max(n, m) + 100
eps = 0.00001
for x in xrange(-nxy, nxy):
for y in xrange(-nxy, nxy):
for b1, b2 in b:
p = (x + b1) * a1 + (y + b2) * a2
abs_p = sqrt(dot(p, p))
sa = dot(p, a) / (abs_a**2)
sc = dot(p, c) / (abs_c**2)
if sa >= 0 and sa < 1 - eps and sc >= 0 and sc < 1 - eps:
r = (cos(2 * pi * sc) * abs_c / (2 * pi),
sin(2 * pi * sc) * abs_c / (2 * pi), sa * abs_a)
at += Atom(element, r)
at.set_cell((2 * abs_c / (2 * pi), 2 * abs_c / (2 * pi), length * abs_a))
b = at.copy()
for i in range(length - 1):
b.translate((0.0, 0.0, abs_a))
for j in b:
at += j
at.center(axis=2)
rcm = at.get_center_of_mass()
at.translate((-rcm[0], -rcm[1], 0))
at.set_pbc((False, False, True))
at.data = nanotube_data(n, m)
return at
def nanotube(n,m,R=1.42,length=1,element='C'):
'''
Create a nanotube around z-axis.
parameters:
-----------
n,m: chiral indices
R: nearest neighbor distance
length: number of unit cells
element: element symbol
'''
from hotbit import Atoms
at = Atoms( pbc = ( False, False, True ) )
sq3 = sqrt(3.0)
a0 = R
gcn = gcd(n, m)
a1 = np.array( [ sq3/2, 0.5 ] ) * a0 * sq3
a2 = np.array( [ sq3/2, -0.5 ] ) * a0 * sq3
h = float(float(n)-float(m))/float(3*gcn)
if h-int(h) == 0.0:
RR = 3
else:
RR = 1
c = n*a1 + m*a2
abs_c = sqrt(dot(c, c))
a = ( -(2*m+n)*a1 + (2*n+m)*a2 )/(gcn*RR)
abs_a = sqrt(dot(a, a))
eps = 0.01
b = [ [ 1./3-eps, 1./3-eps ], [ 2./3-eps, 2./3-eps ] ]
nxy = max(n, m)+100
eps = 0.00001
for x in xrange(-nxy, nxy):
for y in xrange(-nxy, nxy):
for b1, b2 in b:
p = (x+b1)*a1 + (y+b2)*a2
abs_p = sqrt(dot(p, p))
sa = dot(p, a)/(abs_a**2)
sc = dot(p, c)/(abs_c**2)
if sa >= 0 and sa < 1-eps and sc >= 0 and sc < 1-eps:
r = ( cos(2*pi*sc)*abs_c/(2*pi), sin(2*pi*sc)*abs_c/(2*pi), sa*abs_a )
at += Atom( element, r )
at.set_cell( ( 2*abs_c/(2*pi), 2*abs_c/(2*pi), length*abs_a ) )
b = at.copy()
for i in range(length-1):
b.translate( ( 0.0, 0.0, abs_a ) )
for j in b:
at += j
at.center(axis=2)
rcm = at.get_center_of_mass()
at.translate( (-rcm[0],-rcm[1],0) )
at.set_pbc((False,False,True))
at.data = nanotube_data(n,m)
return at