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 setup_bending(atoms, angle, radius, rotation=0.0, physical=True):
"""
Prepare a bending setup for a tube or slab.
Tube should be originally periodic in z-direction with
the correct cell, and optionally periodic in y-direction.
Then atoms are set up for bending with hotbit.Wedge class
with bending wrt. z-axis, and optionally periodic along
z-axis.
Atoms are first rotated pi/2 around -x-axis, then
rotated an angle 'rotation' around y-axis, then
transformed the distance 'radius' towards x-axis.
The atoms are further adjusted for the wedge angle 'angle'.
'physical' tells if the angle should be 2*pi/integer.
"""
a = atoms.copy()
a.rotate('-x', np.pi / 2)
L = a.get_cell().diagonal()
if abs(L.prod() - a.get_volume()) > 1E-10:
raise AssertionError('Cell should be orthorhombic.')
pbc = a.get_pbc()
if not pbc[2] or pbc[0]:
raise AssertionError(
'Should be periodic in z-direction and not periodic in x-direction'
)
r = a.get_positions()
if np.any(r[:, 1] < 0): # index 1 is correct here
raise AssertionError('For bending, all atoms should be above xy-plane')
# move and adjust
a.rotate('y', rotation)
for i in range(len(a)):
x, y = r[i, 0:2]
R = x + radius
phi = y * angle / L[2]
r[i, 0] = R * np.cos(phi)
r[i, 1] = R * np.sin(phi)
a.set_positions(r)
a = Atoms(a, container='Wedge')
a.set_container(angle=angle, height=L[1], pbcz=pbc[1], physical=physical)
return a
def setup_bending(atoms,angle,radius,rotation=0.0,physical=True):
"""
Prepare a bending setup for a tube or slab.
Tube should be originally periodic in z-direction with
the correct cell, and optionally periodic in y-direction.
Then atoms are set up for bending with hotbit.Wedge class
with bending wrt. z-axis, and optionally periodic along
z-axis.
Atoms are first rotated pi/2 around -x-axis, then
rotated an angle 'rotation' around y-axis, then
transformed the distance 'radius' towards x-axis.
The atoms are further adjusted for the wedge angle 'angle'.
'physical' tells if the angle should be 2*pi/integer.
"""
a = atoms.copy()
a.rotate('-x',np.pi/2)
L = a.get_cell().diagonal()
if abs(L.prod()-a.get_volume())>1E-10:
raise AssertionError('Cell should be orthorhombic.')
pbc = a.get_pbc()
if not pbc[2] or pbc[0]:
raise AssertionError('Should be periodic in z-direction and not periodic in x-direction')
r = a.get_positions()
if np.any( r[:,1]<0 ): # index 1 is correct here
raise AssertionError('For bending, all atoms should be above xy-plane')
# move and adjust
a.rotate('y',rotation)
for i in range(len(a)):
x,y = r[i,0:2]
R = x + radius
phi = y*angle/L[2]
r[i,0] = R*np.cos(phi)
r[i,1] = R*np.sin(phi)
a.set_positions(r)
a = Atoms(a,container='Wedge')
a.set_container(angle=angle,height=L[1],pbcz=pbc[1],physical=physical)
return a