from ase import *
from numpy import random, pi
from box import Atoms
from box import mix
from hotbit import Hotbit
#from hotbit import Calculator0
from ase.units import Bohr, Hartree
from hotbit.test.misc import default_param
# C-non-SCC
calc = Hotbit(SCC=False, txt='test.cal', **default_param)
C = Atoms('C', positions=[(0, 0, 0)], cell=(10, 10, 10), pbc=False)
C.center(vacuum=100)
C.set_calculator(calc)
e = C.get_potential_energy()
if abs(e) > 1E-6:
raise RuntimeError('energy %f, should be %f' % (e, 0.0))
# C, SCC
calc = Hotbit(SCC=True, txt='test.cal', **default_param)
C = Atoms('C', positions=[(0, 0, 0)], cell=(10, 10, 10), pbc=False)
C.center(vacuum=100)
C.set_calculator(calc)
e = C.get_potential_energy()
if abs(e) > 1E-6:
raise RuntimeError('energy %f, should be %f' % (e, 0.0))
# rotate Au-dimer
#calc0=Calculator0(SCC=True,txt='test.cal',**default_param)
calc = Hotbit(SCC=True, txt='test.cal', **default_param)
Au2 = Atoms('Au2',
from ase import *
from numpy import random, pi
from box import Atoms
from box import mix
from hotbit import Hotbit
# from hotbit import Calculator0
from ase.units import Bohr, Hartree
from hotbit.test.misc import default_param
# C-non-SCC
calc = Hotbit(SCC=False, txt="test.cal", **default_param)
C = Atoms("C", positions=[(0, 0, 0)], cell=(10, 10, 10), pbc=False)
C.center(vacuum=100)
C.set_calculator(calc)
e = C.get_potential_energy()
if abs(e) > 1e-6:
raise RuntimeError("energy %f, should be %f" % (e, 0.0))
# C, SCC
calc = Hotbit(SCC=True, txt="test.cal", **default_param)
C = Atoms("C", positions=[(0, 0, 0)], cell=(10, 10, 10), pbc=False)
C.center(vacuum=100)
C.set_calculator(calc)
e = C.get_potential_energy()
if abs(e) > 1e-6:
raise RuntimeError("energy %f, should be %f" % (e, 0.0))
# rotate Au-dimer
# calc0=Calculator0(SCC=True,txt='test.cal',**default_param)
plot = False
import numpy as np
from box import mix
from ase.units import Hartree
Na3 = Atoms('Na3',
positions=[(1.69649997, 0, 0), (-1.69649997, 0, 0),
(0, 2.9384241, 0)],
cell=(50, 50, 50),
pbc=False)
tm = mix.Timer()
calc = Hotbit(charge=1, SCC=True, txt='test_lr.cal', **default_param)
Na3.set_calculator(calc)
calc.solve_ground_state(Na3)
lr = LinearResponse(calc)
omega, F = lr.get_linear_response()
e, f = mix.broaden(omega, F, width=0.1)
if plot:
pl.scatter(e2, f2)
pl.plot(e, f, label='python')
pl.legend()
pl.show()
calc = Hotbit(SCC=True, txt='test_lr.cal', **default_param)
C60 = Atoms(read('C60.xyz'))
C60.set_calculator(calc)
calc.solve_ground_state(C60)
try:
import pylab as pl
except:
plot=False
import numpy as np
from box import mix
from ase.units import Hartree
Na3=Atoms('Na3',positions=[(1.69649997,0,0),(-1.69649997,0,0),(0,2.9384241,0)],cell=(50,50,50),pbc=False)
tm=mix.Timer()
calc=Hotbit(charge=1,SCC=True,txt='test_lr.cal',**default_param)
Na3.set_calculator(calc)
calc.solve_ground_state(Na3)
lr=LinearResponse(calc)
omega,F=lr.get_linear_response()
e,f=mix.broaden(omega,F,width=0.1)
if plot:
pl.scatter(e2,f2)
pl.plot(e,f,label='python')
pl.legend()
pl.show()
calc=Hotbit(SCC=True,txt='test_lr.cal',**default_param)
C60=Atoms(read('C60.xyz'))
C60.set_calculator(calc)
calc.solve_ground_state(C60)
def get_positions(self):
positions = np.empty((self.M * self.N, 3))
n1 = 0
for image in self.images:
n2 = n1 + self.N
positions[n1:n2] = image.get_positions()
n1 = n2
return positions
if __name__ == '__main__':
fmax = 1E-4
calc = Hotbit(potential='neb_model_1')
first = Atoms(symbols='H', positions=[(3.0, -1.3, 0.0)]) #,(0,0,0)])
first.set_calculator(calc)
md.quench_atoms(first, fmax=fmax)
print('first minimum:', first.get_positions()[0])
last = Atoms('H', [(0.77, 1.31, 0.0)]) #,(0,0,0)])
last.set_calculator(calc)
md.quench_atoms(last, fmax=fmax)
print('last minimum:', last.get_positions()[0])
images = [first.copy() for x in range(10)]
images.append(last)
bti = BTI(images, calc)
bti.initial_interpolation()
qn = ase.MDMin(bti, dt=0.05)
writer = md.TrajectoryWriter(images, name='test')
def get_positions(self):
positions = np.empty((self.M*self.N,3))
n1 = 0
for image in self.images:
n2 = n1 + self.N
positions[n1:n2] = image.get_positions()
n1 = n2
return positions
if __name__=='__main__':
fmax=1E-4
calc=Hotbit(potential='neb_model_1')
first=Atoms(symbols='H',positions=[(3.0,-1.3,0.0)]) #,(0,0,0)])
first.set_calculator(calc)
md.quench_atoms(first,fmax=fmax)
print 'first minimum:',first.get_positions()[0]
last=Atoms('H',[(0.77,1.31,0.0)]) #,(0,0,0)])
last.set_calculator(calc)
md.quench_atoms(last,fmax=fmax)
print 'last minimum:',last.get_positions()[0]
images=[first.copy() for x in range(10)]
images.append(last)
