from ase_ext import Atoms
from ase_ext.calculators.emt import EMT
from ase_ext.constraints import FixBondLength
from ase_ext.io import PickleTrajectory
from ase_ext.optimize import BFGS
a = 3.6
b = a / 2
cu = Atoms('Cu2Ag',
positions=[(0, 0, 0), (b, b, 0), (a, a, b)],
calculator=EMT())
e0 = cu.get_potential_energy()
print(e0)
d0 = cu.get_distance(0, 1)
cu.set_constraint(FixBondLength(0, 1))
t = PickleTrajectory('cu2ag.traj', 'w', cu)
qn = BFGS(cu)
qn.attach(t.write)
def f():
print(cu.get_distance(0, 1))
qn.attach(f)
qn.run(fmax=0.01)
assert abs(cu.get_distance(0, 1) - d0) < 1e-14
from ase_ext import Atoms
from ase_ext.calculators.emt import EMT
from ase_ext.optimize import QuasiNewton
n2 = Atoms('N2', positions=[(0, 0, 0), (0, 0, 1.1)], calculator=EMT())
QuasiNewton(n2).run(0.01)
print(n2.get_distance(0, 1), n2.get_potential_energy())
from ase_ext import Atom, Atoms
m = Atoms('H2')
a = m[0]
b = Atom('H')
for c in [a, b]:
assert c.x == 0
c.z = 24.0
assert c.position[2] == 24.0
assert c.symbol == 'H'
c.number = 92
assert c.symbol == 'U'
c.symbol = 'Fe'
assert c.number == 26
c.tag = 42
assert c.tag == 42
c.momentum = (1,2,3)
assert m[0].tag == 42
momenta = m.get_momenta()
m = Atoms('LiH')
for a in m:
print(a.symbol)
for a in m:
if a.symbol == 'H':
a.z = 0.75
assert m.get_distance(0, 1) == 0.75
a = m.pop()
m += a
del m[:1]
print(m)
from math import sqrt, pi
from ase_ext import Atoms
from ase_ext.calculators.emt import EMT
from ase_ext.constraints import FixBondLengths
from ase_ext.optimize import BFGS, QuasiNewton
from ase_ext.neb import SingleCalculatorNEB
from ase_ext.lattice.surface import fcc111, add_adsorbate
from math import sqrt, cos, sin
zpos = cos(134.3 / 2.0 * pi / 180.0) * 1.197
xpos = sin(134.3 / 2.0 * pi / 180.0) * 1.19
co2 = Atoms('COO',
positions=[(-xpos + 1.2, 0, -zpos), (-xpos + 1.2, -1.1, -zpos),
(-xpos + 1.2, 1.1, -zpos)])
slab = fcc111('Au', size=(2, 2, 4), vacuum=2 * 5, orthogonal=True)
slab.center()
add_adsorbate(slab, co2, 1.5, 'bridge')
slab.set_pbc((True, True, False))
d0 = co2.get_distance(-3, -2)
d1 = co2.get_distance(-3, -1)
calc = EMT()
slab.set_calculator(calc)
constraint = FixBondLengths([[-3, -2], [-3, -1]])
slab.set_constraint(constraint)
dyn = BFGS(slab, trajectory='relax.traj')
dyn.run(fmax=0.05)
assert abs(co2.get_distance(-3, -2) - d0) < 1e-14
assert abs(co2.get_distance(-3, -1) - d1) < 1e-14
