def append_dimer(self,
weight,
calc,
R,
comment=None,
label='dimer',
color=None):
"""
Use dimer bond length in fitting.
parameters:
===========
weight: fitting weight
calc: Hotbit calculator used in calculation
(remember Gamma-point and charge)
R: dimer bond length (Angstroms)
comment: fitting comment for par-file (replaced by label if None)
label: plotting label (replaced by comment if None)
color: plotting color
"""
if comment == None: comment = label
self.r_dimer = R
atoms = Atoms([self.sym1, self.sym2], [(0, 0, 0), (R, 0, 0)],
pbc=False)
atoms.center(vacuum=5)
color = self._get_color(color)
self.append_scalable_system(weight,
calc,
atoms,
comment=comment,
label=label,
color=color)
def graphene(n1, n2, R, height=5.0):
"""
Construct graphene lattice, multiply the primitive cell
n1 x n2 times in corresponding directions.
.-----.
/ /
/ X / a2
/ /
X----->
a1
"""
from hotbit import Atoms
if not isinstance(R, float): R = R[0]
a1 = vec([R * np.cos(pi / 6) * 2, 0., 0.])
a2 = 0.5 * a1 + vec([0., 1.5 * R, 0.])
#assert n2%2==0
r = []
for i1 in range(n1):
for i2 in range(n2):
corner = i1 * a1 + i2 * a2
r.append(corner)
r.append(corner + a1 + vec([0.0, R, 0.0]))
cell = [[n1 * a1[0], 0, 0], [n2 * a2[0], n2 * a2[1], 0], [0, 0, 10]]
atoms = Atoms('C' * len(r), positions=r, cell=cell)
atoms.center(vacuum=height / 2, axis=2)
atoms.set_pbc((True, True, False))
return atoms
def graphene(n1,n2,R,height=5.0):
"""
Construct graphene lattice, multiply the primitive cell
n1 x n2 times in corresponding directions.
.-----.
/ /
/ X / a2
/ /
X----->
a1
"""
from hotbit import Atoms
if not isinstance(R,float): R=R[0]
a1=vec([R*np.cos(pi/6)*2,0.,0.])
a2=0.5*a1 + vec([0.,1.5*R,0.])
#assert n2%2==0
r=[]
for i1 in range(n1):
for i2 in range(n2):
corner = i1*a1+i2*a2
r.append(corner)
r.append(corner+a1+vec([0.0,R,0.0]))
cell=[[n1*a1[0], 0, 0],[n2*a2[0],n2*a2[1],0],[0,0,10]]
atoms=Atoms('C'*len(r),positions=r,cell=cell)
atoms.center(vacuum=height/2,axis=2)
atoms.set_pbc((True,True,False))
return atoms
def append_dimer(self,weight,calc,R,comment=None,label='dimer',color=None):
"""
Use dimer bond length in fitting.
parameters:
===========
weight: fitting weight
calc: Hotbit calculator used in calculation
(remember Gamma-point and charge)
R: dimer bond length (Angstroms)
comment: fitting comment for par-file (replaced by label if None)
label: plotting label (replaced by comment if None)
color: plotting color
"""
if comment==None: comment=label
self.r_dimer = R
atoms = Atoms([self.sym1,self.sym2],[(0,0,0),(R,0,0)],pbc=False)
atoms.center(vacuum=5)
color = self._get_color(color)
self.append_scalable_system(weight,calc,atoms,comment=comment,label=label,color=color)
def get_isolated_energies(self, trajs, par):
"""
Return the energies of an isolated atoms.
"""
elements = []
energies = {}
for t in trajs:
traj = PickleTrajectory(t)
for atom in traj[0]:
if not atom.symbol in elements:
elements.append(atom.symbol)
el1, el2 = par.split("_")[0:2]
for el in elements:
ss = "%s%s" % (el, el)
if el1 == el2 and el1 == el:
tables = {ss:par, 'rest':'default'}
calc = Hotbit(SCC=True, tables=tables)
else:
calc = Hotbit(SCC=True)
atoms = Atoms(ss, ((0,0,0),(200,0,0)))
atoms.center(vacuum=100)
atoms.set_calculator(calc)
energies[el] = atoms.get_potential_energy() / 2
return energies
def get_isolated_energies(self, trajs, par):
"""
Return the energies of an isolated atoms.
"""
elements = []
energies = {}
for t in trajs:
traj = PickleTrajectory(t)
for atom in traj[0]:
if not atom.symbol in elements:
elements.append(atom.symbol)
el1, el2 = par.split("_")[0:2]
for el in elements:
ss = "%s%s" % (el, el)
if el1 == el2 and el1 == el:
tables = {ss:par, 'rest':'default'}
calc = Hotbit(SCC=True, tables=tables)
else:
calc = Hotbit(SCC=True)
atoms = Atoms(ss, ((0,0,0),(200,0,0)))
atoms.center(vacuum=100)
atoms.set_calculator(calc)
energies[el] = atoms.get_potential_energy() / 2
return energies
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