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()
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()
# q -= np.sum(q)/len(q)
r = [[SX / 4, SY / 4, SZ / 4], [3 * SX / 4, SY / 4, SZ / 4],
[SX / 4, 3 * SY / 4, SZ / 4], [SX / 4, SY / 4, 3 * SZ / 4]]
q = [1, -1, 1, -1]
if False:
# no periodicity, this should simply not fail
if debug:
print("0D")
a = Atoms('%iH' % NAT,
positions=r,
charges=q,
cell=[SX, SY, SZ],
pbc=False)
b = HotbitAtoms(atoms=a, container='Bravais')
electrostatics_test(b, 3)
electrostatics_test(b, 5)
if True:
# 1D periodicity
if debug:
print("1D")
a = Atoms('%iH' % NAT,
positions=r,
charges=q,
cell=[SX, SY, SZ],
pbc=[False, False, True])
b = HotbitAtoms(atoms=a, container='Bravais')
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
#
# energy conservation
#
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,**default_param)
atoms2.set_calculator(calc)
e2 = atoms.get_potential_energy()
assert abs(e1-e2)<1E-5
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))
for sol in solvers:
if debug:
print("=== %s ===" % sol.__class__)
for name, target_M, nnd, a in systems:
syms = a.get_chemical_symbols()
#a.set_charges([ (Q if sym == syms[0] else -Q) for sym in syms ])
# to work with older versions
a.set_initial_charges([ (-Q,Q)[sym==syms[0]] for sym in syms ])
a.translate([0.25*a0,0.25*a0,0.25*a0])
if debug:
write("%s.cfg" % name, a)
ha = HotbitAtoms(a, container='Bravais')
sol.update(ha, ha.get_initial_charges())
phi = sol.get_potential()
e = np.sum(a.get_initial_charges()*phi)/2
M = -2*e*a0*nnd/(len(a))
err = abs(M-target_M)
if debug:
print("%20s %8.6f %8.6f (%8.6e)" % ( name, M, target_M, err ))
assert err < 1e-3
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
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
chiral.set_container(height=height,angle=2*pi/5)
calc = Hotbit(SCC=SCC,txt='chiral.cal',kpts=(1,1,nkpts),gamma_cut=cut)
chiral.set_calculator(calc)
view(chiral)
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=SCC,txt='chiral.cal',width=0.1,kpts=(1,1,1),gamma_cut=cut) #,verbose_SCC=True)
chiral.set_calculator(calc)
assert check_energy_conservation(chiral,dt=0.5*fs,steps=50,tol=0.02,plot=True)
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,
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
for sol in solvers:
if debug:
print "=== %s ===" % sol.__class__
for name, target_M, nnd, a in systems:
syms = a.get_chemical_symbols()
#a.set_charges([ (Q if sym == syms[0] else -Q) for sym in syms ])
# to work with older versions
a.set_initial_charges([ (-Q,Q)[sym==syms[0]] for sym in syms ])
a.translate([0.25*a0,0.25*a0,0.25*a0])
if debug:
write("%s.cfg" % name, a)
ha = HotbitAtoms(a, container='Bravais')
sol.update(ha, ha.get_initial_charges())
phi = sol.get_potential()
e = np.sum(a.get_initial_charges()*phi)/2
M = -2*e*a0*nnd/(len(a))
err = abs(M-target_M)
if debug:
print "%20s %8.6f %8.6f (%8.6e)" % ( name, M, target_M, err )
assert err < 1e-3
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))
c2 = Hotbit(SCC=SCC,txt='-',kpts=(1,1,1),gamma_cut=cut,**default_param)
a2.set_calculator(c2)
[ SX/4, 3*SY/4, SZ/4 ],
[ SX/4, SY/4, 3*SZ/4 ] ]
q = [ 1, -1, 1, -1 ]
if False:
# no periodicity, this should simply not fail
if debug:
print "0D"
a = Atoms('%iH' % NAT,
positions = r,
charges = q,
cell = [ SX, SY, SZ ],
pbc = False
)
b = HotbitAtoms(
atoms = a,
container = 'Bravais'
)
electrostatics_test(b, 3)
electrostatics_test(b, 5)
if True:
# 1D periodicity
if debug:
print "1D"
a = Atoms('%iH' % NAT,
positions = r,
charges = q,
cell = [ SX, SY, SZ ],
pbc = [ False, False, True ]