from ase import *
from hotbit import *
from numpy import *
from box.systems import nanotube
# testing chiral
atoms = nanotube('C',1.42,5,0)
atoms = Atoms(atoms,container='Chiral')
atoms.set_container(angle=0.0)
traj=PickleTrajectory('tmp.trj','w',atoms)
for angle in concatenate( (linspace(0,pi/2,50),linspace(pi/2,0,50)) ):
atoms.set_container(angle=angle,scale_atoms=True)
traj.write()
h = atoms.get_cell()[2,2]
for height in concatenate( (linspace(h,2*h,59),linspace(2*h,h,50)) ):
atoms.set_container(height=height,scale_atoms=True)
traj.write()
for height,angle in zip( linspace(h,2*h),linspace(0,pi/4,50) ):
atoms.set_container(angle=angle,height=height,scale_atoms=True)
traj.write()
# testing wedge
atoms = Atoms('C2',[(2,0,0),(2.5,1,1)],container='Wedge')
atoms.set_container(angle=pi/4,height=2.0)
traj=PickleTrajectory('tmp2.trj','w',atoms)
for height in concatenate( (linspace(2,4,50),linspace(4,2,50)) ):
from ase import *
from hotbit import *
from numpy import *
from box.systems import nanotube
# testing chiral
atoms = nanotube('C', 1.42, 5, 0)
atoms = Atoms(atoms, container='Chiral')
atoms.set_container(angle=0.0)
traj = PickleTrajectory('tmp.trj', 'w', atoms)
for angle in concatenate((linspace(0, pi / 2, 50), linspace(pi / 2, 0, 50))):
atoms.set_container(angle=angle, scale_atoms=True)
traj.write()
h = atoms.get_cell()[2, 2]
for height in concatenate((linspace(h, 2 * h, 59), linspace(2 * h, h, 50))):
atoms.set_container(height=height, scale_atoms=True)
traj.write()
for height, angle in zip(linspace(h, 2 * h), linspace(0, pi / 4, 50)):
atoms.set_container(angle=angle, height=height, scale_atoms=True)
traj.write()
# testing wedge
atoms = Atoms('C2', [(2, 0, 0), (2.5, 1, 1)], container='Wedge')
atoms.set_container(angle=pi / 4, height=2.0)
traj = PickleTrajectory('tmp2.trj', 'w', atoms)
for height in concatenate((linspace(2, 4, 50), linspace(4, 2, 50))):
atoms.set_container(height=height, scale_atoms=True)
traj.write()
from ase import *
from hotbit import *
from numpy import *
from box.systems import nanotube
atoms = nanotube(9,0)
angle = atoms.container.get('angle')
traj = PickleTrajectory('twisting.traj','w',atoms)
# twist without scaling
for twist in linspace(0,pi/10,100):
atoms.set_container(angle=angle+twist)
traj.write()
# twist with scaling
atoms.set_container(angle=angle)
for twist in linspace(0,pi/10,100):
atoms.set_container(angle=angle+twist,scale_atoms=True)
traj.write()
# twist with scaling + view copies
cp = atoms.extended_copy((1,1,10))
traj = PickleTrajectory('twisting_extended.traj','w',cp)
atoms.set_container(angle=angle,scale_atoms=True)
for twist in linspace(0,pi/10,100):
atoms.set_container(angle=angle+twist,scale_atoms=True)
cp.set_positions( atoms.extended_copy((1,1,10)).get_positions() )
traj.write()
from ase import *
from hotbit import *
from numpy import *
from box.systems import nanotube
atoms = nanotube(9, 0)
angle = atoms.container.get('angle')
traj = PickleTrajectory('twisting.traj', 'w', atoms)
# twist without scaling
for twist in linspace(0, pi / 10, 100):
atoms.set_container(angle=angle + twist)
traj.write()
# twist with scaling
atoms.set_container(angle=angle)
for twist in linspace(0, pi / 10, 100):
atoms.set_container(angle=angle + twist, scale_atoms=True)
traj.write()
# twist with scaling + view copies
cp = atoms.extended_copy((1, 1, 10))
traj = PickleTrajectory('twisting_extended.traj', 'w', cp)
atoms.set_container(angle=angle, scale_atoms=True)
for twist in linspace(0, pi / 10, 100):
atoms.set_container(angle=angle + twist, scale_atoms=True)
cp.set_positions(atoms.extended_copy((1, 1, 10)).get_positions())
traj.write()
from ase import *
from hotbit import *
from hotbit.atoms import Atoms
from box.systems import nanotube
from box.md import check_energy_conservation
nkpts=10
SCC=True
cut=5.0
# check that SCC works for chiral atoms
# energy of normal infinite (5,0)
straight = nanotube('C',1.42,5,0)
straight.set_pbc((False,False,True))
for i in range(len(straight)):
if straight[i].z<1.0:
r=sqrt(straight[i].x**2+straight[i].y**2)
c=(1+r)/r
x,y,z = c*straight[i].x,c*straight[i].y,straight[i].z
straight+=Atom('H',(x,y,z))
#view(straight)
calc = Hotbit(SCC=SCC,txt='chiral.cal',kpts=(1,1,nkpts),gamma_cut=cut)
straight.set_calculator(calc)
e1 = straight.get_potential_energy()
# same thing, but calculate by twisting 2*pi/5 while translating
height = straight.get_cell()[2,2]
chiral = Atoms(container='Chiral')
chiral += straight
from ase import * from hotbit import * from math import pi from hotbit.atoms import Atoms from box.systems import nanotube from box.md import check_energy_conservation nkpts=10 # energy of normal infinite (5,0) straight = nanotube(5,0,1.42) calc = Hotbit(SCC=False,txt='chiral.cal',kpts=(1,1,nkpts)) straight.set_calculator(calc) e1 = straight.get_potential_energy() #view(straight) # same thing, but calculate by twisting 2*pi/5 while translating height = straight.get_cell()[2,2] chiral = Atoms(container='Chiral') chiral += straight chiral.set_container(height=height,angle=2*pi/5) calc = Hotbit(SCC=False,txt='chiral.cal',kpts=(1,1,nkpts)) chiral.set_calculator(calc) e2 = chiral.get_potential_energy() assert abs(e1-e2)<1E-6 # check the energy conservation for the chiral situation #chiral.rattle(0.1) #calc = Hotbit(SCC=False,txt='chiral.cal',kpts=(1,1,1))
