def _update_atoms(self, atoms):
""" Update atoms-object, whether it is ase.Atoms or hotbit.Atoms. """
if hasattr(atoms, 'container'):
self.atoms = atoms.copy()
else:
container = container_magic(atoms)
#print 'cc',container
atoms_cont = Atoms(atoms=atoms, container=container)
self.atoms = atoms_cont.copy()
x3, y3 = calc.get_covalent_energy('atoms', i=1, j=1)
assert abs((y1 + y2 + y3).sum() - y.sum()) < eps
sm = 0.0
for i in range(calc.st.norb):
for j in range(i, calc.st.norb):
x1, y1 = calc.get_covalent_energy('orbitals', i=i, j=j)
sm += y1.sum()
assert abs(y.sum() - sm) < eps
if True:
# check that C1H1-presentation of C6H6 goes right
n1 = 4
SCC = True
cut = 1E10
a1 = Atoms('CH', [(1.42, 0, 0), (2.42, 0.1, 0.1)], container='Wedge')
a1.set_container(M=6, height=10)
aux = a1.extended_copy([(1, 0, 0)])
a1 += aux
a1.set_container(M=3, height=10)
n2 = 12
c1 = Hotbit(SCC=SCC,
txt='-',
kpts=(3, 1, 1),
gamma_cut=cut,
**default_param)
a1.set_calculator(c1)
a1.get_potential_energy()
a2 = a1.extended_copy((3, 1, 1))
from ase import *
from ase import Atoms as ase_Atoms
from hotbit import *
from hotbit.atoms import Atoms
from box.md import check_energy_conservation
from hotbit.test.misc import default_param
SCC = True
cut = 3.0
atoms = Atoms('CH', [(1.42, 0, 0), (2.42, 0, 0)], 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()
aux = atoms.extended_copy((3, 1, 1))
atoms2 = Atoms(container='Wedge')
atoms2 += aux[0]
atoms2 += aux[-1]
atoms2.set_container(M=6, height=10)
#view(atoms2)
calc = Hotbit(SCC=SCC,
txt='tmp.cal',
kpts=(6, 1, 1),
gamma_cut=cut,
import ase.units as units
from ase import *
from ase import Atoms as ase_Atoms
from hotbit import *
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
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)) #chiral.set_calculator(calc) #conv = check_energy_conservation(chiral,dt=0.5*fs,steps=50,tol=0.01,plot=False) #assert conv