def extended_copy(self,n):
""" Get copies of atoms for all listed symmetry operations n.
@param: n i) list of 3-tuples for transformations explicitly
e.g. [(0,0,0),(1,0,0),(0,1,0)]
ii) 3-tuple for the number of transformations
(for infinite extensions -> start from zero;
for finite extensions -> symmetry ops around zero)
e.g. (10,10,1)
iii) 3-tuple of 2-tuples that give the ranges for symmetry ops
e.g. ((-3,3),(-3,3),1)
Return normal ase.Atoms -instance.
"""
r = self.container.get_symmetry_operation_ranges()
if isinstance(n,list):
n_list = copy(n)
elif isinstance(n,tuple):
ops = []
for i in range(3):
if isinstance(n[i],tuple):
ops.append( np.arange(n[i][0],n[i][1]+1) )
elif isinstance(n[i],int):
assert n[i]>0
if r[i,0]==-np.Inf:
# this symmetry operation has the full range
rng = np.arange(0,n[i])
else:
# take copies around the 0-operation
start = max(r[i,0],-n[i]//2)
rng = np.arange(start,start+n[i])
ops.append( rng )
n_list=[]
for n1 in ops[0]:
for n2 in ops[1]:
for n3 in ops[2]:
n_list.append( (n1,n2,n3) )
atoms2=None
for n in n_list:
self._check_symmetry_operation(n)
atomsn = ase_Atoms()
atomsn += self
atomsn.set_positions( np.array([self.transform(r,n) for r in self.get_positions()]) )
try:
atoms2 += atomsn
except:
atoms2 = atomsn
atoms2.set_pbc(False)
atoms2.set_cell((1,1,1))
return atoms2
def extended_copy(self,n):
""" Get copies of atoms for all listed symmetry operations n.
@param: n i) list of 3-tuples for transformations explicitly
e.g. [(0,0,0),(1,0,0),(0,1,0)]
ii) 3-tuple for the number of transformations
(for infinite extensions -> start from zero;
for finite extensions -> symmetry ops around zero)
e.g. (10,10,1)
iii) 3-tuple of 2-tuples that give the ranges for symmetry ops
e.g. ((-3,3),(-3,3),1)
Return normal ase.Atoms -instance.
"""
r = self.container.get_symmetry_operation_ranges()
if isinstance(n,list):
n_list = copy(n)
elif isinstance(n,tuple):
ops = []
for i in range(3):
if isinstance(n[i],tuple):
ops.append( np.arange(n[i][0],n[i][1]+1) )
elif isinstance(n[i],int):
assert n[i]>0
if r[i,0]==-np.Inf:
# this symmetry operation has the full range
rng = np.arange(0,n[i])
else:
# take copies around the 0-operation
start = max(r[i,0],-n[i]/2)
rng = np.arange(start,start+n[i])
ops.append( rng )
n_list=[]
for n1 in ops[0]:
for n2 in ops[1]:
for n3 in ops[2]:
n_list.append( (n1,n2,n3) )
atoms2=None
for n in n_list:
self._check_symmetry_operation(n)
atomsn = ase_Atoms()
atomsn += self
atomsn.set_positions( np.array([self.transform(r,n) for r in self.get_positions()]) )
try:
atoms2 += atomsn
except:
atoms2 = atomsn
atoms2.set_pbc(False)
atoms2.set_cell((1,1,1))
return atoms2
def armchair_ribbon(n1, n2, R, pbc='z'):
"""
Make ribbon out of graphene with armchair edges: n1 armchair periods in x-direction
and n2 stacked armchairs.
parameters:
===========
n1: length (units in periodic direction)
n2: width
R: bond distance
pbc: periodic direction ('z' or 'x')
"""
from hotbit import Atoms
a1 = vec([3 * R, 0, 0])
a2 = vec([0, 2 * R * np.cos(pi / 6), 0])
atoms = ase_Atoms()
r = []
for i1 in range(n1):
for i2 in range(n2):
corner = i1 * a1 + i2 * a2
atoms += Atom('C', corner)
atoms += Atom('C', corner + vec([R, 0, 0]))
atoms += Atom('C', corner + vec([1.5 * R, R * np.cos(pi / 6), 0]))
atoms += Atom('C', corner + vec([2.5 * R, R * np.cos(pi / 6), 0]))
if pbc == 'x':
atoms.set_cell([n1 * 3 * R, n2 * 2 * R * np.cos(pi / 6), 1])
atoms.center(vacuum=5, axis=2)
atoms.center(vacuum=5, axis=1)
atoms.set_pbc((True, False, False))
return atoms
elif pbc == 'z':
atoms.translate(-atoms.get_center_of_mass())
atoms.rotate('z', np.pi / 2)
atoms.rotate('x', np.pi / 2)
atoms.center(vacuum=5, axis=1)
atoms.translate(-atoms.get_center_of_mass())
zmin = atoms.get_positions()[:, 2].min()
atoms.translate((0, 0, -zmin))
atoms.set_cell([n2 * 2 * R * np.cos(pi / 6), 1, n1 * 3 * R])
atoms.set_pbc((False, False, True))
return atoms
else:
raise NotImplementedError('pbc only along x or z')
def armchair_ribbon(n1,n2,R,pbc='z'):
"""
Make ribbon out of graphene with armchair edges: n1 armchair periods in x-direction
and n2 stacked armchairs.
parameters:
===========
n1: length (units in periodic direction)
n2: width
R: bond distance
pbc: periodic direction ('z' or 'x')
"""
from hotbit import Atoms
a1=vec([3*R,0,0])
a2=vec([0,2*R*np.cos(pi/6),0])
atoms=ase_Atoms()
r=[]
for i1 in range(n1):
for i2 in range(n2):
corner=i1*a1+i2*a2
atoms += Atom('C',corner)
atoms += Atom('C',corner+vec([R,0,0]))
atoms += Atom('C',corner+vec([1.5*R,R*np.cos(pi/6),0]))
atoms += Atom('C',corner+vec([2.5*R,R*np.cos(pi/6),0]))
if pbc=='x':
atoms.set_cell( [n1*3*R,n2*2*R*np.cos(pi/6),1] )
atoms.center(vacuum=5,axis=2)
atoms.center(vacuum=5,axis=1)
atoms.set_pbc((True,False,False))
return atoms
elif pbc=='z':
atoms.translate( -atoms.get_center_of_mass() )
atoms.rotate('z',np.pi/2)
atoms.rotate('x',np.pi/2)
atoms.center(vacuum=5,axis=1)
atoms.translate( -atoms.get_center_of_mass() )
zmin = atoms.get_positions()[:,2].min()
atoms.translate( (0,0,-zmin) )
atoms.set_cell( [n2*2*R*np.cos(pi/6),1,n1*3*R] )
atoms.set_pbc((False,False,True))
return atoms
else:
raise NotImplementedError('pbc only along x or z')
def ZGNR(n, units=1, pbc='z', R=1.42):
"""
Make an n-zigzag graphene nanoribbon.
parameters:
===========
n: ribbon width (atomic rows)
length: ribbon length (unit cells)
pbc: periodic direction, 'x' or 'z'
R: bond length
"""
from hotbit import Atoms
a0 = R * np.sqrt(3)
atoms = ase_Atoms()
for i in range(n):
x = 1
if np.mod(i, 2) == 1:
x = -1
atoms += Atom('C', (0, 3 * R * i / 2 + 3 * R / 4 - x * R / 4, 0))
atoms += Atom('C', (a0 / 2, 3 * R * i / 2 + 3 * R / 4 + x * R / 4, 0))
a = atoms.copy()
for i in range(units - 1):
b = a.copy()
b.translate(((i + 1) * a0, 0, 0))
atoms += b
if pbc == 'x':
atoms.set_pbc((True, False, False))
atoms.set_cell((units * a0, 1, 1))
atoms.center(vacuum=6, axis=1)
atoms.center(vacuum=6, axis=2)
elif pbc == 'z':
atoms.set_pbc((False, False, True))
atoms.rotate('z', np.pi / 2)
atoms.rotate('x', np.pi / 2)
atoms.set_cell((n * 3 * R / 2 * 1.2 / 2, 1, units * a0))
atoms.translate(-atoms.get_center_of_mass())
atoms.center(axis=2)
return atoms
def ZGNR(n,units=1,pbc='z',R=1.42):
"""
Make an n-zigzag graphene nanoribbon.
parameters:
===========
n: ribbon width (atomic rows)
length: ribbon length (unit cells)
pbc: periodic direction, 'x' or 'z'
R: bond length
"""
from hotbit import Atoms
a0 = R*np.sqrt(3)
atoms = ase_Atoms()
for i in range(n):
x = 1
if np.mod(i,2)==1:
x=-1
atoms += Atom('C',(0,3*R*i/2+3*R/4-x*R/4,0))
atoms += Atom('C',(a0/2,3*R*i/2+3*R/4+x*R/4,0))
a = atoms.copy()
for i in range(units-1):
b = a.copy()
b.translate(((i+1)*a0,0,0))
atoms += b
if pbc=='x':
atoms.set_pbc((True,False,False))
atoms.set_cell((units*a0,1,1))
atoms.center(vacuum=6,axis=1)
atoms.center(vacuum=6,axis=2)
elif pbc=='z':
atoms.set_pbc((False,False,True))
atoms.rotate('z',np.pi/2)
atoms.rotate('x',np.pi/2)
atoms.set_cell((n*3*R/2*1.2/2,1,units*a0))
atoms.translate( -atoms.get_center_of_mass() )
atoms.center(axis=2)
return atoms
def AGNR(n, units=1, pbc='z', R=1.42):
"""
Make an n-armchair graphene nanoribbon.
parameters:
===========
n: ribbon width (atomic rows)
length: ribbon length (unit cells)
pbc: periodic direction, 'x' or 'z'
R: bond length
"""
from hotbit import Atoms
a = R * np.sqrt(3)
atoms = ase_Atoms()
for i in range(n):
x0 = 0.0
if np.mod(i, 2) == 1:
x0 = 1.5 * R
atoms += Atom('C', (x0 + 0, i * a / 2, 0))
atoms += Atom('C', (x0 + R, i * a / 2, 0))
a = atoms.copy()
for i in range(units - 1):
b = a.copy()
b.translate(((i + 1) * 3 * R, 0, 0))
atoms += b
if pbc == 'x':
atoms.set_pbc((True, False, False))
atoms.set_cell((units * 3 * R, 1, 1))
atoms.center(vacuum=6, axis=1)
atoms.center(vacuum=6, axis=2)
elif pbc == 'z':
atoms.set_pbc((False, False, True))
atoms.rotate('z', np.pi / 2)
atoms.rotate('x', np.pi / 2)
atoms.set_cell((1, 1, units * 3 * R))
atoms.translate(-atoms.get_center_of_mass())
return atoms
def AGNR(n,units=1,pbc='z',R=1.42):
"""
Make an n-armchair graphene nanoribbon.
parameters:
===========
n: ribbon width (atomic rows)
length: ribbon length (unit cells)
pbc: periodic direction, 'x' or 'z'
R: bond length
"""
from hotbit import Atoms
a = R*np.sqrt(3)
atoms = ase_Atoms()
for i in range(n):
x0 = 0.0
if np.mod(i,2)==1:
x0 = 1.5*R
atoms += Atom('C',(x0+0,i*a/2,0))
atoms += Atom('C',(x0+R,i*a/2,0))
a = atoms.copy()
for i in range(units-1):
b = a.copy()
b.translate(((i+1)*3*R,0,0))
atoms += b
if pbc=='x':
atoms.set_pbc((True,False,False))
atoms.set_cell((units*3*R,1,1))
atoms.center(vacuum=6,axis=1)
atoms.center(vacuum=6,axis=2)
elif pbc=='z':
atoms.set_pbc((False,False,True))
atoms.rotate('z',np.pi/2)
atoms.rotate('x',np.pi/2)
atoms.set_cell((1,1,units*3*R))
atoms.translate( -atoms.get_center_of_mass() )
return atoms
def zigzag_ribbon(n1, n2, R, pbc='z'):
"""
Make ribbon out of graphene with zigzag edges.
"""
from hotbit import Atoms
a1 = vec([2 * R * np.cos(pi / 6), 0, 0])
a2 = vec([0, 3 * R, 0])
r = []
for i1 in range(n1):
for i2 in range(n2):
corner = i1 * a1 + i2 * a2
r.append(corner + vec([R * np.cos(pi / 6), R / 2, 0]))
r.append(corner + vec([0, R, 0]))
r.append(corner + vec([0, 2 * R, 0]))
r.append(corner + vec([R * np.cos(pi / 6), 2.5 * R, 0]))
cell = [n1 * 2 * R * np.cos(pi / 6), n2 * 3 * R, 1]
elements = ['C'] * len(r)
atoms = ase_Atoms(elements, r, cell=cell)
if pbc == 'x':
atoms.set_cell([2 * R * np.cos(pi / 6), n1 * 3 * R, 1])
atoms.center(vacuum=5, axis=2)
atoms.center(vacuum=5, axis=1)
atoms.set_pbc((True, False, False))
return atoms
elif pbc == 'z':
atoms.translate(-atoms.get_center_of_mass())
atoms.rotate('z', np.pi / 2)
atoms.rotate('x', np.pi / 2)
atoms.center(vacuum=5, axis=1)
atoms.translate(-atoms.get_center_of_mass())
zmin = atoms.get_positions()[:, 2].min()
atoms.translate((0, 0, -zmin))
atoms.set_cell([n2 * 2 * R * np.cos(pi / 6), 1, n1 * 3 * R])
atoms.set_pbc((False, False, True))
return atoms
else:
raise NotImplementedError('pbc only along x or z')
def zigzag_ribbon(n1,n2,R,pbc='z'):
"""
Make ribbon out of graphene with zigzag edges.
"""
from hotbit import Atoms
a1=vec([2*R*np.cos(pi/6),0,0])
a2=vec([0,3*R,0])
r=[]
for i1 in range(n1):
for i2 in range(n2):
corner=i1*a1+i2*a2
r.append(corner+vec([R*np.cos(pi/6),R/2,0]))
r.append(corner+vec([0,R,0]))
r.append(corner+vec([0,2*R,0]))
r.append(corner+vec([R*np.cos(pi/6),2.5*R,0]))
cell=[n1*2*R*np.cos(pi/6),n2*3*R,1]
elements=['C']*len(r)
atoms = ase_Atoms(elements,r,cell=cell)
if pbc=='x':
atoms.set_cell( [2*R*np.cos(pi/6),n1*3*R,1] )
atoms.center(vacuum=5,axis=2)
atoms.center(vacuum=5,axis=1)
atoms.set_pbc((True,False,False))
return atoms
elif pbc=='z':
atoms.translate( -atoms.get_center_of_mass() )
atoms.rotate('z',np.pi/2)
atoms.rotate('x',np.pi/2)
atoms.center(vacuum=5,axis=1)
atoms.translate( -atoms.get_center_of_mass() )
zmin = atoms.get_positions()[:,2].min()
atoms.translate( (0,0,-zmin) )
atoms.set_cell( [n2*2*R*np.cos(pi/6),1,n1*3*R] )
atoms.set_pbc((False,False,True))
return atoms
else:
raise NotImplementedError('pbc only along x or z')
from hotbit.atoms import Atoms
from box.md import check_energy_conservation
from hotbit.test.misc import default_param
# check that C1H1-presentation of C6H6 goes right
SCC=True
cut=3.0
atoms = Atoms('CH',[(1.42,0,0),(2.0,1.0,0.2)],container='Wedge')
atoms.set_container(M=6,height=10)
calc = Hotbit(SCC=SCC,txt='tmp.cal',kpts=(6,1,1),gamma_cut=cut,**default_param)
atoms.set_calculator(calc)
e1 = atoms.get_potential_energy()
atoms6 = ase_Atoms(pbc=False)
atoms6 += atoms.extended_copy([(i-2,0,0) for i in range(6)])
#view(atoms)
calc = Hotbit(SCC=SCC,txt='tmp.cal',gamma_cut=cut,**default_param)
atoms6.set_calculator(calc)
e6 = atoms6.get_potential_energy()
assert abs(6*e1-e6)<1E-5
#
# energy conservation
#
atoms = Atoms('CH',[(1.42,0,0),(2.0,0.5,0.3)],container='Wedge')
atoms.set_container(M=6,height=10)
calc = Hotbit(SCC=SCC,txt='tmp.cal',kpts=(6,1,1),gamma_cut=cut,**default_param)
# check that C1H1-presentation of C6H6 goes right
SCC = True
cut = 3.0
atoms = Atoms('CH', [(1.42, 0, 0), (2.0, 1.0, 0.2)], container='Wedge')
atoms.set_container(M=6, height=10)
calc = Hotbit(SCC=SCC,
txt='tmp.cal',
kpts=(6, 1, 1),
gamma_cut=cut,
**default_param)
atoms.set_calculator(calc)
e1 = atoms.get_potential_energy()
atoms6 = ase_Atoms(pbc=False)
atoms6 += atoms.extended_copy([(i - 2, 0, 0) for i in range(6)])
#view(atoms)
calc = Hotbit(SCC=SCC, txt='tmp.cal', gamma_cut=cut, **default_param)
atoms6.set_calculator(calc)
e6 = atoms6.get_potential_energy()
assert abs(6 * e1 - e6) < 1E-5
#
# energy conservation
#
atoms = Atoms('CH', [(1.42, 0, 0), (2.0, 0.5, 0.3)], container='Wedge')
atoms.set_container(M=6, height=10)
calc = Hotbit(SCC=SCC,
txt='tmp.cal',