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)
atoms.set_calculator(calc)
atoms.rattle(0.1)
assert check_energy_conservation(atoms,dt=0.2*units.fs,steps=30,tol=0.01,plot=False)
# Relax (twist) the structure
q = optimize.FIRE(atoms,trajectory='polyethene.trj',logfile=None)
q.run(fmax=0.5)
# Displace atoms from their equilibrium positions and check forces
atoms.rattle(0.1)
# Check electrostatics only
# atoms.set_initial_charges([1.0,1.0,1.0,1.0,-1.0,-1.0,-1.0,-1.0])
# atoms.set_calculator(calc.st.es)
# Check forces from finite differences
ffd, f0, err = check_forces(atoms, dx=1e-6)
if debug:
print "Finite differences forces:"
print ffd
print "Analytical forces:"
print f0
print "Difference:"
print abs(ffd-f0)
print "Error:"
print err
assert err < 1e-5
# Check energy conservation from a molecular dynamics run
assert check_energy_conservation(atoms,dt=0.25*units.fs,steps=100,
tol=0.01,plot=debug)
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)
from ase import *
from hotbit import *
from box.md import check_energy_conservation
from ase import io
M = 7
atoms = Atoms('Au2', [(5, 0, 0), (5, 2.5, 0.3)], container='Wedge')
atoms.set_container(M=M, height=5.0)
calc = Hotbit(SCC=False, txt='-', kpts=(M, 1, 1))
atoms.set_calculator(calc)
e1 = atoms.get_potential_energy()
whole = atoms.extended_copy((M, 1, 1))
calc = Hotbit(SCC=False, txt='-')
whole.set_calculator(calc)
e2 = whole.get_potential_energy()
assert abs(M * e1 - e2) < 1E-10
assert check_energy_conservation(atoms,
dt=2.5 * units.fs,
steps=50,
tol=0.01,
plot=False)
#dyn = VelocityVerlet(atoms,2.5*fs)
#traj = PickleTrajectory('koe.traj','w',atoms)
#dyn.attach(traj.write)
#dyn.run(100)
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)
q = optimize.FIRE(atoms, trajectory='polyethene.trj', logfile=None)
q.run(fmax=0.5)
# Displace atoms from their equilibrium positions and check forces
atoms.rattle(0.1)
# Check electrostatics only
# atoms.set_initial_charges([1.0,1.0,1.0,1.0,-1.0,-1.0,-1.0,-1.0])
# atoms.set_calculator(calc.st.es)
# Check forces from finite differences
ffd, f0, err = check_forces(atoms, dx=1e-6)
if debug:
print "Finite differences forces:"
print ffd
print "Analytical forces:"
print f0
print "Difference:"
print abs(ffd - f0)
print "Error:"
print err
assert err < 1e-5
# Check energy conservation from a molecular dynamics run
assert check_energy_conservation(atoms,
dt=0.25 * units.fs,
steps=100,
tol=0.01,
plot=debug)