try:
from pylab import *
except:
pass
from ase import Atoms as ase_Atoms
from hotbit import *
from hotbit.atoms import Atoms
from hotbit.test.misc import default_param
from numpy import *
from box.systems import graphene
from ase.data.molecules import molecule
eps = 1E-6
if True:
atoms = graphene(2, 2, 1.42)
calc = Hotbit(SCC=False, kpts=(4, 4, 1), txt='-', **default_param)
atoms.set_calculator(calc)
atoms.get_potential_energy()
# compare to Fig.4 of Koskinen & Makinen, CMS 47, 237 (2009)
if False:
w = 0.2
x, y = calc.get_covalent_energy('default', width=w, window=(-20, 15))
plot(x, y, label='total')
axhline(0)
x, y = calc.get_covalent_energy('angmom',
i=0,
j=0,
width=w,
window=(-20, 15))
from ase import *
from hotbit import *
from box.md import check_energy_conservation
from box.systems import graphene
from numpy import *
from hotbit.test.misc import default_param
R=1.416552
nkpts = 10
# graphene's cohesion energy
atoms=graphene(2,2,R)
atoms=Atoms('C2',[(0,0,0),(2*cos(pi/6)*R,R,0)],pbc=(True,True,False),\
cell=array([[2*cos(pi/6)*R,0,0],[R*cos(pi/6),R*1.5,0],[0,0,5]]) )
calc=Hotbit(SCC=False,txt='graphene.cal',kpts=(nkpts,nkpts,1),**default_param)
atoms.set_calculator(calc)
coh = atoms.get_potential_energy()/2
assert abs(-9.626283-coh)<1E-6
# energy conservation
atoms[0].z+=0.1
calc=Hotbit(SCC=False,txt='graphene.cal',kpts=(3,3,1),**default_param)
atoms.set_calculator(calc)
assert check_energy_conservation(atoms,dt=0.5*units.fs,steps=30,tol=1E-2,plot=False)
import ase.units as units
from ase import *
from hotbit import *
from box.md import check_energy_conservation
from box.systems import graphene
from numpy import *
from hotbit.test.misc import default_param
R=1.416552
nkpts = 10
# graphene's cohesion energy
atoms=graphene(2,2,R)
atoms=Atoms('C2',[(0,0,0),(2*cos(pi/6)*R,R,0)],pbc=(True,True,False),\
cell=array([[2*cos(pi/6)*R,0,0],[R*cos(pi/6),R*1.5,0],[0,0,5]]) )
calc=Hotbit(SCC=False,txt='graphene.cal',kpts=(nkpts,nkpts,1),**default_param)
atoms.set_calculator(calc)
coh = atoms.get_potential_energy()/2
assert abs(-9.626283-coh)<1E-5
# energy conservation
atoms[0].z+=0.1
calc=Hotbit(SCC=False,txt='graphene.cal',kpts=(3,3,1),**default_param)
atoms.set_calculator(calc)
assert check_energy_conservation(atoms,dt=0.5*units.fs,steps=30,tol=1E-2,plot=False)
try:
from pylab import *
except:
pass
from ase import Atoms as ase_Atoms
from hotbit import *
from hotbit.atoms import Atoms
from hotbit.test.misc import default_param
from numpy import *
from box.systems import graphene
from ase.data.molecules import molecule
eps = 1E-6
if True:
atoms = graphene(2,2,1.42)
calc = Hotbit(SCC=False,kpts=(4,4,1),txt='-',**default_param)
atoms.set_calculator(calc)
atoms.get_potential_energy()
# compare to Fig.4 of Koskinen & Makinen, CMS 47, 237 (2009)
if False:
w=0.2
x,y = calc.get_covalent_energy('default',width=w,window=(-20,15))
plot(x,y,label='total')
axhline(0)
x,y = calc.get_covalent_energy('angmom',i=0,j=0,width=w,window=(-20,15))
plot(x,y,label='ss')
x,y = calc.get_covalent_energy('angmom',i=0,j=1,width=w,window=(-20,15))
plot(x,y,label='sp')
x,y = calc.get_covalent_energy('angmom',i=1,j=1,width=w,window=(-20,15))
