def lmp_structure(self):
ribbon=graphene(dict(latx=self.gnrx,laty=self.gnry,latz=1,gnrtype=self.gnrtype)).lmp_structure()
gnt=GNT(dict(latx=self.latx,laty=self.laty,latz=1,type=self.gnttype))
atoms=gnt.lmp_structure()
self.center_box(atoms)
self.center_box(ribbon)
ribbon.rotate('z',self.angle)
r=gnt.radius+self.bond
for atom in ribbon:
atom.position=gnt.trans(atom.position,r=r)
max=atoms.positions[:,0].max()
min=atoms.positions[:,0].min()
del ribbon[ribbon.positions[:,0]>max]
del ribbon[ribbon.positions[:,0]<min]
ribbon.translate([0,0,-r])
atoms.extend(ribbon)
atoms.center(vacuum=10)
return atoms
def lmp_structure(self):
ribbon=graphene(dict(latx=self.gnrx,laty=self.gnry,latz=1,gnrtype=self.gnrtype)).lmp_structure()
gnt=GNT(dict(latx=self.latx,laty=self.laty,latz=1,type=self.gnttype))
atoms=gnt.lmp_structure()
self.center_box(atoms)
self.center_box(ribbon)
ribbon.rotate('z',self.angle)
r=gnt.radius+self.bond
for atom in ribbon:
atom.position=gnt.trans(atom.position,r=r)
max=atoms.positions[:,0].max()
min=atoms.positions[:,0].min()
del ribbon[ribbon.positions[:,0]>max]
del ribbon[ribbon.positions[:,0]<min]
ribbon.translate([0,0,-r])
atoms.extend(ribbon)
atoms.center(vacuum=10)
return atoms
def ori_structure(self):
atoms = graphene(dict(latx=self.latx, laty=self.laty,
latz=self.latz)).lmp_structure()
self.center_box(atoms)
for atom in atoms:
atom.position = self.trans(atom.position)
pair = atoms.copy()
if self.tripair:
pair.rotate('y', pi)
pair.translate([0, 0, -4])
gnt = GNT(dict(latx=4, laty=10, xp=0)).lmp_structure()
self.center_box(gnt)
gnt.translate([0, 0, -2])
atoms.extend(gnt)
atoms.extend(pair)
self.swap(atoms, 1)
atoms.rotate('x', pi / 2)
else:
pair.rotate('z', pi / 2)
pair.rotate('y', pi)
pair.translate([0, 0, 10])
atoms.extend(pair)
self.swap(atoms, 1)
dx = 7
xlo = atoms.positions[:, 0].min() + dx
xhi = atoms.positions[:, 0].max() - dx
ylo = atoms.positions[:, 1].min() + dx
yhi = atoms.positions[:, 1].max() - dx
zlo = atoms.positions[:, 2].min() + dx
zhi = atoms.positions[:, 2].max() - dx
right0 = atoms.positions[:, 2] > zhi
right1 = atoms.positions[:, 2] < zlo
if self.tripair:
right0 = atoms.positions[:, 1] > yhi
right1 = atoms.positions[:, 1] < ylo
self.x1z1 = np.arange(len(atoms), dtype='int')[np.logical_and(
atoms.positions[:, 0] > xhi, right0)] + 1
self.x1z0 = np.arange(len(atoms), dtype='int')[np.logical_and(
atoms.positions[:, 0] > xhi, right1)] + 1
self.x0y1 = np.arange(len(atoms), dtype='int')[np.logical_and(
atoms.positions[:, 0] < xlo, atoms.positions[:, 1] > yhi)] + 1
self.x0y0 = np.arange(len(atoms), dtype='int')[np.logical_and(
atoms.positions[:, 0] < xlo, atoms.positions[:, 1] < ylo)] + 1
self.fmag = self.strain / float(len(self.x1z1))
g = self.angle / 2.0
d = self.angle1 / 2.0
r0 = [cos(g), 0.0, sin(g)]
r1 = [cos(g), 0.0, -sin(g)]
if self.tripair:
r0 = [cos(g), sin(g), 0.0]
r1 = [cos(g), -sin(g), 0.0]
self.posx1z1 = np.array((50, 50, 50)) + 500 * np.array(r0)
self.posx1z0 = np.array((50, 50, 50)) + 500 * np.array(r1)
self.posx0y1 = np.array(
(50, 50, 50)) + 500 * np.array([-cos(d), sin(d), 0.0])
self.posx0y0 = np.array(
(50, 50, 50)) + 500 * np.array([-cos(d), -sin(d), 0.0])
atoms.center(vacuum=50)
return atoms
def ori_structure(self):
atoms=graphene(dict(latx=self.latx,laty=self.laty,latz=self.latz)).lmp_structure()
self.center_box(atoms)
for atom in atoms:
atom.position=self.trans(atom.position)
pair=atoms.copy()
if self.tripair:
pair.rotate('y',pi)
pair.translate([0,0,-4])
gnt=GNT(dict(latx=4,laty=10,xp=0)).lmp_structure()
self.center_box(gnt)
gnt.translate([0,0,-2])
atoms.extend(gnt)
atoms.extend(pair)
self.swap(atoms,1)
atoms.rotate('x',pi/2)
else:
pair.rotate('z',pi/2)
pair.rotate('y',pi)
pair.translate([0,0,10])
atoms.extend(pair)
self.swap(atoms,1)
dx=7
xlo=atoms.positions[:,0].min()+dx
xhi=atoms.positions[:,0].max()-dx
ylo=atoms.positions[:,1].min()+dx
yhi=atoms.positions[:,1].max()-dx
zlo=atoms.positions[:,2].min()+dx
zhi=atoms.positions[:,2].max()-dx
right0=atoms.positions[:,2]>zhi
right1=atoms.positions[:,2]<zlo
if self.tripair:
right0=atoms.positions[:,1]>yhi
right1=atoms.positions[:,1]<ylo
self.x1z1=np.arange(len(atoms),dtype='int')[np.logical_and(atoms.positions[:,0]>xhi , right0)]+1
self.x1z0=np.arange(len(atoms),dtype='int')[np.logical_and(atoms.positions[:,0]>xhi , right1)]+1
self.x0y1=np.arange(len(atoms),dtype='int')[np.logical_and(atoms.positions[:,0]<xlo , atoms.positions[:,1]>yhi)]+1
self.x0y0=np.arange(len(atoms),dtype='int')[np.logical_and(atoms.positions[:,0]<xlo , atoms.positions[:,1]<ylo)]+1
self.fmag=self.strain/float(len(self.x1z1))
g=self.angle/2.0
d=self.angle1/2.0
r0=[cos(g),0.0,sin(g)]
r1=[cos(g),0.0,-sin(g)]
if self.tripair:
r0=[cos(g),sin(g),0.0]
r1=[cos(g),-sin(g),0.0]
self.posx1z1=np.array((50,50,50))+500*np.array(r0)
self.posx1z0=np.array((50,50,50))+500*np.array(r1)
self.posx0y1=np.array((50,50,50))+500*np.array([-cos(d),sin(d),0.0])
self.posx0y0=np.array((50,50,50))+500*np.array([-cos(d),-sin(d),0.0])
atoms.center(vacuum=50)
return atoms
def lmp_structure(self):
atoms=Twist(dict(latx=self.latx,laty=self.laty,latz=1,gnrtype=self.gnrtype,twist=pi)).lmp_structure()
self.writeatoms(atoms,'twist')
r=atoms.cell[0,0]/2/pi
gnt=GNT()
self.center_box(atoms)
atoms.rotate('z',pi/2)
for atom in atoms:
atom.position=gnt.trans(atom.position,r=r)
#atoms.rotate('y',pi/2)
atoms.center(vacuum=10)
return atoms
def lmp_structure(self):
ribbon=graphene(dict(latx=self.gnrx,laty=self.gnry,latz=1,gnrtype=self.gnrtype)).lmp_structure()
length=ribbon.cell[0][0]
gnt=GNT(dict(latx=self.gntx,laty=self.gnty,latz=1,type=self.gnttype))
atoms=gnt.lmp_structure()
self.center_box(atoms)
self.center_box(ribbon)
atoms.rotate('z',pi/2)
left=atoms.copy()
r=gnt.radius+self.bond
d=(length-2*pi*r)/2
left.translate([-d/2,0,0])
atoms.translate([d/2,0,0])
for atom in ribbon:
atom.position=self.trans(atom.position,r=r,d=d)
atoms.extend(ribbon)
atoms.extend(left)
atoms.center(vacuum=10)
return atoms
def lmp_structure(self):
ribbon = graphene(
dict(latx=self.gnrx, laty=self.gnry, latz=1,
gnrtype=self.gnrtype)).lmp_structure()
length = ribbon.cell[0][0]
gnt = GNT(
dict(latx=self.gntx, laty=self.gnty, latz=1, type=self.gnttype))
atoms = gnt.lmp_structure()
self.center_box(atoms)
self.center_box(ribbon)
atoms.rotate('z', pi / 2)
left = atoms.copy()
r = gnt.radius + self.bond
d = (length - 2 * pi * r) / 2
left.translate([-d / 2, 0, 0])
atoms.translate([d / 2, 0, 0])
for atom in ribbon:
atom.position = self.trans(atom.position, r=r, d=d)
atoms.extend(ribbon)
atoms.extend(left)
atoms.center(vacuum=10)
return atoms
def lmp_structure(self):
atoms=GNT(dict(latx=self.latx,laty=self.laty,latz=1,gnrtype=self.gnrtype,phi=self.angle)).lmp_structure()
r=atoms.cell[0,0]/self.phi
gnt=GNT()
self.center_box(atoms)
atoms.rotate('z',pi/2)
for atom in atoms:
atom.position=gnt.trans(atom.position,r=r)
#atoms.rotate('y',pi/2)
atoms.center(vacuum=10)
return atoms
def lmp_structure(self):
atoms = GNT(dict(latx=self.latx, laty=5, latz=1,
gnrtype=self.gnrtype)).lmp_structure()
self.center_box(atoms)
x = atoms.cell[0, 0] / 2
c60 = molecule('C60', data=extra_molecules.data)
c60.rotate('z', 2 * pi / 5)
c60.rotate('y', -pi / 4)
right = c60[c60.positions[:, 0] > c60.cell[0, 0] / 2].copy()
del c60[c60.positions[:, 0] > c60.cell[0, 0] / 2]
c60.translate([-x, 0, 0])
right.translate([x, 0, 0])
atoms.extend(c60)
atoms.extend(right)
atoms.center(vacuum=10)
return atoms
def lmp_structure(self):
atoms = GNT(
dict(latx=self.latx,
laty=self.laty,
latz=1,
gnrtype=self.gnrtype,
phi=self.angle)).lmp_structure()
r = atoms.cell[0, 0] / self.phi
gnt = GNT()
self.center_box(atoms)
atoms.rotate('z', pi / 2)
for atom in atoms:
atom.position = gnt.trans(atom.position, r=r)
#atoms.rotate('y',pi/2)
atoms.center(vacuum=10)
return atoms
def lmp_structure(self):
atoms=GNT(dict(latx=self.latx,laty=5,latz=1,gnrtype=self.gnrtype)).lmp_structure()
self.center_box(atoms)
x=atoms.cell[0,0]/2
c60=molecule('C60',data=extra_molecules.data)
c60.rotate('z',2*pi/5)
c60.rotate('y',-pi/4)
right=c60[c60.positions[:,0]>c60.cell[0,0]/2].copy()
del c60[c60.positions[:,0]>c60.cell[0,0]/2]
c60.translate([-x,0,0])
right.translate([x,0,0])
atoms.extend(c60)
atoms.extend(right)
atoms.center(vacuum=10)
return atoms