def bhopt(atoms=None,
gen='poscar.gen',
fmax=0.3,
step=100,
dr=0.5,
temperature=100,
optimizer=BFGS,
vdwnn=False,
nn=True,
v=False):
if atoms is None:
atoms = read(gen)
atoms.calc = IRFF(atoms=atoms,
libfile='ffield.json',
rcut=None,
nn=nn,
vdwnn=vdwnn)
optimizer = BasinHopping(
atoms=atoms, # the system to optimize
temperature=temperature * kB, # 'temperature' to overcome barriers
dr=dr, # maximal stepwidth
optimizer=optimizer,
fmax=fmax, # maximal force for the optimizer
trajectory="opt.traj")
optimizer.run(step)
if v:
images = Trajectory('opt.traj')
view(images[-1])
return atoms
def test_basin():
# Global minima from
# Wales and Doye, J. Phys. Chem. A, vol 101 (1997) 5111-5116
E_global = {4: -6.000000, 5: -9.103852, 6: -12.712062, 7: -16.505384}
N = 7
R = N**(1. / 3.)
np.random.seed(42)
pos = np.random.uniform(-R, R, (N, 3))
s = Atoms('He' + str(N), positions=pos)
s.calc = LennardJones()
original_positions = 1. * s.get_positions()
ftraj = 'lowest.traj'
for GlobalOptimizer in [
BasinHopping(s,
temperature=100 * kB,
dr=0.5,
trajectory=ftraj,
optimizer_logfile=None)
]:
if isinstance(GlobalOptimizer, BasinHopping):
GlobalOptimizer.run(10)
Emin, smin = GlobalOptimizer.get_minimum()
else:
GlobalOptimizer(totalsteps=10)
Emin = s.get_potential_energy()
smin = s
print("N=", N, 'minimal energy found', Emin, ' global minimum:',
E_global[N])
# recalc energy
smin.calc = LennardJones()
E = smin.get_potential_energy()
assert abs(E - Emin) < 1e-15
other = read(ftraj)
E2 = other.get_potential_energy()
assert abs(E2 - Emin) < 1e-15
# check that only minima were written
last_energy = None
for im in io.read(ftraj, index=':'):
energy = im.get_potential_energy()
if last_energy is not None:
assert energy < last_energy
last_energy = energy
# reset positions
s.set_positions(original_positions)
#!/usr/bin/env python
from ase import Atoms, Atom
from ase.calculators.aims import Aims, AimsCube
from ase.cluster.icosahedron import Icosahedron
from ase.io.aims import read_aims
from ase.optimize.basin import BasinHopping
from ase.optimize import LBFGS
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
atoms = Icosahedron('Pt', noshells=1)
calc = Aims(label='cluster/pt-isosahedron-1-bh',
xc='pbe',
spin='none',
relativistic = 'atomic_zora scalar',
sc_accuracy_etot=1e-5,
sc_accuracy_eev=1e-3,
sc_accuracy_rho=1e-4,
sc_accuracy_forces=1e-3)
atoms.set_calculator(calc)
bh = BasinHopping(atoms)
bh.run(temperature=100 * kB, # 'temperature' to overcome barriers
dr=0.5, # maximal stepwidth
optimizer=LBFGS, # optimizer to find local minima
fmax=0.1# maximal force for the optimizer
)
7: -16.505384,
}
N = 7
R = N**(1. / 3.)
np.random.seed(42)
pos = np.random.uniform(-R, R, (N, 3))
s = Atoms('He' + str(N), positions=pos)
s.set_calculator(LennardJones())
original_positions = 1. * s.get_positions()
ftraj = 'lowest.traj'
for GlobalOptimizer in [
BasinHopping(s,
temperature=100 * kB,
dr=0.5,
trajectory=ftraj,
optimizer_logfile=None),
]:
if str(GlobalOptimizer.__class__) == 'ase.optimize.basin.BasinHopping':
GlobalOptimizer.run(10)
Emin, smin = GlobalOptimizer.get_minimum()
else:
GlobalOptimizer(totalsteps=10)
Emin = s.get_potential_energy()
smin = s
print "N=", N, 'minimal energy found', Emin,
print ' global minimum:', E_global[N]
# recalc energy
from ase import Atoms, Atom
from ase.calculators.aims import Aims
from ase.cluster.decahedron import Decahedron
from ase.optimize.basin import BasinHopping
from ase.units import kB
from ase.optimize import LBFGS
atoms = Decahedron('Pt',
p=2, # natoms on 100 face normal to 5-fold axis
q=1, # natoms 0n 100 parallel to 5-fold axis
r=0) # depth of the Marks re-entrance?
calc = Aims(label='cluster/pt-decahedron-2-1-bh',
xc='pbe',
spin='none',
relativistic = 'atomic_zora scalar',
sc_accuracy_etot=1e-5,
sc_accuracy_eev=1e-3,
sc_accuracy_rho=1e-4,
sc_accuracy_forces=1e-3)
atoms.set_calculator(calc)
bh = BasinHopping(atoms = atoms,
temperature=100 * kB, # 'temperature' to overcome barriers
dr=0.5, # maximal stepwidth
optimizer=LBFGS, # optimizer to find local minima
fmax=0.1
)
bh.run(10)
#!/usr/bin/env python
from ase import Atoms, Atom
from jasp import *
from ase.cluster.icosahedron import Icosahedron
from ase.optimize.basin import BasinHopping
from ase.units import kB
from ase.optimize import LBFGS
atoms = Atoms('Pt3', ([0, 0, 0], [0, 0, 2.0], [0, 2.0, 0.0]),
cell=(8, 8, 8))
with jasp('cluster/pt3',
xc='PBE',
encut=450,
kpts=[5, 5, 5],
ismear=0,
sigma=0.01, # this is small for a molecule
ibrion=2, # conjugate gradient optimizer
nsw=500, # do at least 5 steps to relax
ediff=1e-5, # set precise energies
atoms=atoms) as calc:
bh = BasinHopping(atoms = atoms,
temperature=100 * kB, # 'temperature' to overcome barriers
dr=0.5, # maximal stepwidth
optimizer=LBFGS, # optimizer to find local minima
fmax=0.1
)
bh.run(100)
from ase.calculators.lj import LennardJones
from ase.optimize.basin import BasinHopping
from ase.io import PickleTrajectory, read
from ase.units import kB
N = 7
R = N**(1./3.)
pos = np.random.uniform(-R, R, (N, 3))
s = Atoms('He' + str(N),
positions = pos)
s.set_calculator(LennardJones())
ftraj = 'lowest.traj'
traj = PickleTrajectory(ftraj, 'w', s)
bh = BasinHopping(s,
temperature=100 * kB, dr=0.5,
optimizer_logfile=None)
bh.attach(traj)
bh.run(10)
Emin, smin = bh.get_minimum()
# recalc energy
smin.set_calculator(LennardJones())
E = smin.get_potential_energy()
assert abs(E - Emin) < 1e-15
traj.close()
smim = read(ftraj)
E = smin.get_potential_energy()
assert abs(E - Emin) < 1e-15
from math import pi, sqrt
from ase import Atoms
from ase.calculators.lj import LennardJones
from ase.optimize.basin import BasinHopping
from ase.io import PickleTrajectory, read
from ase.units import kB
N = 7
R = N**(1. / 3.)
pos = np.random.uniform(-R, R, (N, 3))
s = Atoms('He' + str(N), positions=pos)
s.set_calculator(LennardJones())
ftraj = 'lowest.traj'
traj = PickleTrajectory(ftraj, 'w', s)
bh = BasinHopping(s, temperature=100 * kB, dr=0.5, optimizer_logfile=None)
bh.attach(traj)
bh.run(10)
Emin, smin = bh.get_minimum()
# recalc energy
smin.set_calculator(LennardJones())
E = smin.get_potential_energy()
assert abs(E - Emin) < 1e-15
traj.close()
smim = read(ftraj)
E = smin.get_potential_energy()
assert abs(E - Emin) < 1e-15
#view(smin)