1import numpy as np
2import pytest
3from ase import Atoms, io
4from ase.calculators.lj import LennardJones
5from ase.optimize.basin import BasinHopping
6from ase.io import read
7from ase.units import kB
8
9
10@pytest.mark.slow
11def test_basin(testdir):
12    # Global minima from
13    # Wales and Doye, J. Phys. Chem. A, vol 101 (1997) 5111-5116
14    E_global = {
15        4: -6.000000,
16        5: -9.103852,
17        6: -12.712062,
18        7: -16.505384}
19    N = 7
20    R = N**(1. / 3.)
21    np.random.seed(42)
22    pos = np.random.uniform(-R, R, (N, 3))
23    s = Atoms('He' + str(N),
24              positions=pos)
25    s.calc = LennardJones()
26    original_positions = 1. * s.get_positions()
27
28    ftraj = 'lowest.traj'
29
30    with BasinHopping(s,
31                      temperature=100 * kB,
32                      dr=0.5,
33                      trajectory=ftraj,
34                      optimizer_logfile=None) as GlobalOptimizer:
35        GlobalOptimizer.run(10)
36        Emin, smin = GlobalOptimizer.get_minimum()
37        print("N=", N, 'minimal energy found', Emin,
38              ' global minimum:', E_global[N])
39
40        # recalc energy
41        smin.calc = LennardJones()
42        E = smin.get_potential_energy()
43        assert abs(E - Emin) < 1e-15
44        other = read(ftraj)
45        E2 = other.get_potential_energy()
46        assert abs(E2 - Emin) < 1e-15
47
48        # check that only minima were written
49        last_energy = None
50        for im in io.read(ftraj, index=':'):
51            energy = im.get_potential_energy()
52            if last_energy is not None:
53                assert energy < last_energy
54            last_energy = energy
55
56        # reset positions
57        s.set_positions(original_positions)
58