def chiral_nanotube(n, m, R=1.42, element='C'):
"""
Construct a nanotube with a chiral container.
parameters:
===========
n,m: chiral indices
R: bond length
element: element type
"""
from hotbit import Atoms
a = np.sqrt(3) * R
a1 = np.array([a, 0, 0])
a2 = np.array([0.5 * a, -1.5 * R, 0])
rl = []
shift = (a / 2, -0.5 * R, 0)
for i in range(n):
origin = i * a1
rl.append(origin)
rl.append(origin + shift)
for j in range(m):
origin = (n - 1) * a1 + (j + 1) * a1
rl.append(origin)
rl.append(origin + shift)
atoms = Atoms()
C = n * a1 + m * a2
Cn = np.linalg.norm(C)
T = np.array([C[1], -C[0], 0])
t = T / np.linalg.norm(T)
radius = Cn / (2 * pi)
atoms = Atoms()
for r in rl:
phi = np.dot(r, C) / Cn**2 * 2 * pi
atoms += Atom(
element,
(radius * np.cos(phi), radius * np.sin(phi), np.dot(r, t)))
atoms = Atoms(atoms, container='Chiral')
height = np.abs(np.dot(a1 - a2, t))
angle = -np.dot(a1 - a2, C) / Cn**2 * 2 * pi
atoms.set_container(angle=angle, height=height)
data = nanotube_data(n, m, R)
T, Ntot = data['T'], 2 * data['hexagons_per_cell']
data['height'] = height
data['twist'] = angle
atoms.data = data
return atoms
def chiral_nanotube(n,m,R=1.42,element='C'):
"""
Construct a nanotube with a chiral container.
parameters:
===========
n,m: chiral indices
R: bond length
element: element type
"""
from hotbit import Atoms
a = np.sqrt(3)*R
a1 = np.array([a,0,0])
a2 = np.array([0.5*a,-1.5*R,0])
rl = []
shift = (a/2,-0.5*R,0)
for i in range(n):
origin = i*a1
rl.append( origin )
rl.append( origin+shift )
for j in range(m):
origin = (n-1)*a1 + (j+1)*a1
rl.append( origin )
rl.append( origin + shift )
atoms = Atoms()
C = n*a1 + m*a2
Cn = np.linalg.norm(C)
T = np.array([C[1],-C[0],0])
t = T/np.linalg.norm(T)
radius = Cn/(2*pi)
atoms = Atoms()
for r in rl:
phi = np.dot(r,C)/Cn**2 * 2*pi
atoms += Atom( element,(radius*np.cos(phi),radius*np.sin(phi),np.dot(r,t)) )
atoms = Atoms(atoms,container='Chiral')
height = np.abs( np.dot(a1-a2,t) )
angle = -np.dot(a1-a2,C)/Cn**2 * 2*pi
atoms.set_container(angle=angle,height=height)
data = nanotube_data(n,m,R)
T, Ntot = data['T'],2*data['hexagons_per_cell']
data['height']=height
data['twist']=angle
atoms.data = data
return atoms
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