def ori_structure(self): lead1=self.lead1=graphene(dict(latx=1,laty=self.laty,latz=1)).lmp_structure() n=len(lead1) center=graphene(dict(latx=self.latx,laty=self.laty,latz=1)).lmp_structure() center.translate(lead1.cell[0]) lead2=lead1.copy() lead2.translate(lead1.cell[0]+center.cell[0]) atoms=Atoms() atoms.extend(lead1) atoms.extend(center) atoms.extend(lead2) atoms.cell=center.cell atoms.cell[0]=lead1.cell[0]+center.cell[0]+lead2.cell[0] lx=self.extent(atoms)[0] self.getScale(lx/2) self.center_box(atoms) self.writeatoms(atoms,'graphene') low=atoms.positions[:,0].min()+2 hi=atoms.positions[:,0].max()-2 self.leftgroup=np.arange(len(atoms),dtype='int')[:n]+1 self.rightgroup=np.arange(len(atoms),dtype='int')[-n:]+1 self.fmag=self.strain/float(len(self.leftgroup)) self.posleft=atoms.positions[self.leftgroup[0]-1].copy()+(50,50,50) self.posright=atoms.positions[self.rightgroup[0]-1].copy()+(50,50,50) self.posleft[0]*=10 self.posright[0]*=10 for atom in atoms: atom.position=self.trans(atom.position) atoms.center(vacuum=50) 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 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 lmp_structure(self): ribbon=graphene(dict(latx=self.latx,laty=self.laty,latz=1,gnrtype=self.gnrtype)).lmp_structure() for atom in ribbon: atom.position=self.trans(atom.position) atoms=Atoms() atoms.extend(ribbon) atoms.center(vacuum=10) return atoms
def lmp_structure(self): ribbon=graphene(dict(latx=self.latx,laty=self.laty,latz=1,gnrtype=self.gnrtype)).lmp_structure() for atom in ribbon: atom.position=self.trans(atom.position) atoms=Atoms() atoms.extend(ribbon) atoms.center(vacuum=10) return atoms
def lmp_structure(self): ribbon=graphene(dict(latx=self.latx,laty=self.laty,latz=1,gnrtype=self.gnrtype)).lmp_structure() self.writeatoms(ribbon,'ribbon') self.length=ribbon.cell[0,0] self.center_box(ribbon) for atom in ribbon: atom.position=self.trans(atom.position) atoms=ribbon atoms.center(vacuum=10,axis=[1,2]) atoms.center(axis=[0]) 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):
ribbon = graphene(
dict(latx=self.latx, laty=self.laty, latz=1,
gnrtype=self.gnrtype)).lmp_structure()
self.writeatoms(ribbon, 'ribbon')
self.length = ribbon.cell[0, 0]
self.center_box(ribbon)
for atom in ribbon:
atom.position = self.trans(atom.position)
atoms = ribbon
atoms.center(vacuum=10, axis=[1, 2])
atoms.center(axis=[0])
return atoms
def lmp_structure(self):
atoms = Atoms()
unit = graphene(
dict(
latx=2,
laty=1,
latz=1,
gnrtype='zigzag')).lmp_structure()
# del unit[unit.positions[:,0].argsort()[-2:]]
ly = unit.cell[1][1]
lidx = unit.positions[:, 0].argsort()[0]
left_of_unit = unit[lidx].position
# the center must be assign because the atoms are centered
unit.rotate('y', 30.0 / 180 * np.pi, center=left_of_unit)
ridx = unit.positions[:, 0].argsort()[-1]
right_of_unit = unit[ridx].position
unit1 = unit.copy()
unit1.rotate('y', 120.0 / 180 * np.pi, center=right_of_unit)
ridx1 = unit1.positions[:, 0].argsort()[-1]
right_of_unit1 = unit1[ridx1].position
# cell[0,0]
lx = right_of_unit1[0] - left_of_unit[0]
unit2 = unit.copy()
# translate unit2 but don't traslate along y
deta = right_of_unit1 - right_of_unit + [0, 0, 1.42 * np.sqrt(3) / 2]
deta[1] = 0
unit2.translate(deta)
lidx2 = unit2.positions[:, 0].argsort()[0]
left_of_unit2 = unit2.positions[lidx2]
unit3 = unit2.copy()
unit3.rotate('y', 120.0 / 180 * np.pi, center=left_of_unit2)
lz = left_of_unit2[2] - right_of_unit[2] + 1.42 * np.sqrt(3) / 2
atoms.extend(unit)
atoms.extend(unit1)
atoms.extend(unit2)
atoms.extend(unit3)
atoms.set_cell([lx, ly, lz])
# important for distance calculation,default all False
atoms.set_pbc([True] * 3)
atoms.center()
atoms = atomic.get_unique_atoms(atoms)
# prevent xs~=1.0
atoms.translate([0.01, 0, 0])
atomic.wrap(atoms)
return atoms
def lmp_structure(self):
atoms = graphene(
dict(latx=self.latx,
laty=self.laty,
latz=self.latz,
gnrtype=self.type)).lmp_structure()
atomic.center_box(atoms)
self.radius = atoms.cell[1][1] / self.phi
for atom in atoms:
atom.position = self.trans(atom.position, r=self.radius)
atoms.center(vacuum=10, axis=[1, 2])
atoms.center(axis=[0])
return atoms
def lmp_structure(self):
atoms = graphene(
dict(
latx=self.latx,
laty=self.laty,
latz=self.latz,
gnrtype=self.type)).lmp_structure()
atomic.center_box(atoms)
self.radius = atoms.cell[1][1] / self.phi
for atom in atoms:
atom.position = self.trans(atom.position, r=self.radius)
atoms.center(vacuum=10, axis=[1, 2])
atoms.center(axis=[0])
return atoms
def ori_structure(self):
lead1 = self.lead1 = graphene(dict(latx=1, laty=self.laty,
latz=1)).lmp_structure()
n = len(lead1)
center = graphene(dict(latx=self.latx, laty=self.laty,
latz=1)).lmp_structure()
center.translate(lead1.cell[0])
lead2 = lead1.copy()
lead2.translate(lead1.cell[0] + center.cell[0])
atoms = Atoms()
atoms.extend(lead1)
atoms.extend(center)
atoms.extend(lead2)
atoms.cell = center.cell
atoms.cell[0] = lead1.cell[0] + center.cell[0] + lead2.cell[0]
lx = self.extent(atoms)[0]
self.getScale(lx / 2)
self.center_box(atoms)
self.writeatoms(atoms, 'graphene')
low = atoms.positions[:, 0].min() + 2
hi = atoms.positions[:, 0].max() - 2
self.leftgroup = np.arange(len(atoms), dtype='int')[:n] + 1
self.rightgroup = np.arange(len(atoms), dtype='int')[-n:] + 1
self.fmag = self.strain / float(len(self.leftgroup))
self.posleft = atoms.positions[self.leftgroup[0] - 1].copy() + (50, 50,
50)
self.posright = atoms.positions[self.rightgroup[0] -
1].copy() + (50, 50, 50)
self.posleft[0] *= 10
self.posright[0] *= 10
for atom in atoms:
atom.position = self.trans(atom.position)
atoms.center(vacuum=50)
return atoms
def lmp_structure(self):
atoms = Atoms()
unit = graphene(dict(latx=2, laty=1, latz=1,
gnrtype='zigzag')).lmp_structure()
# del unit[unit.positions[:,0].argsort()[-2:]]
ly = unit.cell[1][1]
lidx = unit.positions[:, 0].argsort()[0]
left_of_unit = unit[lidx].position
# the center must be assign because the atoms are centered
unit.rotate('y', 30.0 / 180 * np.pi, center=left_of_unit)
ridx = unit.positions[:, 0].argsort()[-1]
right_of_unit = unit[ridx].position
unit1 = unit.copy()
unit1.rotate('y', 120.0 / 180 * np.pi, center=right_of_unit)
ridx1 = unit1.positions[:, 0].argsort()[-1]
right_of_unit1 = unit1[ridx1].position
# cell[0,0]
lx = right_of_unit1[0] - left_of_unit[0]
unit2 = unit.copy()
# translate unit2 but don't traslate along y
deta = right_of_unit1 - right_of_unit + [0, 0, 1.42 * np.sqrt(3) / 2]
deta[1] = 0
unit2.translate(deta)
lidx2 = unit2.positions[:, 0].argsort()[0]
left_of_unit2 = unit2.positions[lidx2]
unit3 = unit2.copy()
unit3.rotate('y', 120.0 / 180 * np.pi, center=left_of_unit2)
lz = left_of_unit2[2] - right_of_unit[2] + 1.42 * np.sqrt(3) / 2
atoms.extend(unit)
atoms.extend(unit1)
atoms.extend(unit2)
atoms.extend(unit3)
atoms.set_cell([lx, ly, lz])
# important for distance calculation,default all False
atoms.set_pbc([True] * 3)
atoms.center()
atoms = atomic.get_unique_atoms(atoms)
# prevent xs~=1.0
atoms.translate([0.01, 0, 0])
atomic.wrap(atoms)
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=20,laty=3,latz=1,gnrtype='zigzag')).lmp_structure()
self.length=ribbon.cell[0,0]
self.center_box(ribbon)
self.w=.2
self.getW(self.length/2)
newlx=2*self.phase(self.length/2,self.w)
for atom in ribbon:
atom.position=self.trans(atom.position)
atoms=ribbon
#atoms.center(vacuum=10,axis=[1,2])
#atoms.cell[0,0]=newlx
#atoms.center(axis=[0])
newatoms=Atoms()
for i in range(4):
atoms.rotate('z',i*pi/2,center=[0,-newlx/4,0])
newatoms.extend(atoms.copy())
newatoms.cell[0,0]=newatoms.cell[1,1]=newlx
newatoms.center()
atoms=newatoms#.repeat([self.latx,self.laty,1])
return atoms
def lmp_structure(self):
ribbon = graphene(dict(latx=20, laty=3, latz=1,
gnrtype='zigzag')).lmp_structure()
self.length = ribbon.cell[0, 0]
self.center_box(ribbon)
self.w = .2
self.getW(self.length / 2)
newlx = 2 * self.phase(self.length / 2, self.w)
for atom in ribbon:
atom.position = self.trans(atom.position)
atoms = ribbon
#atoms.center(vacuum=10,axis=[1,2])
#atoms.cell[0,0]=newlx
#atoms.center(axis=[0])
newatoms = Atoms()
for i in range(4):
atoms.rotate('z', i * pi / 2, center=[0, -newlx / 4, 0])
newatoms.extend(atoms.copy())
newatoms.cell[0, 0] = newatoms.cell[1, 1] = newlx
newatoms.center()
atoms = newatoms #.repeat([self.latx,self.laty,1])
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
