def test_bee(xc, testdir):
"""Check BEEF ensemble code."""
size = 7 # size of ensemble
# From a calculator:
calc = BEECalculator(xc)
ens = BEEFEnsemble(calc)
energies = ens.get_ensemble_energies(size)
assert energies.shape == (size, )
# From a file:
ens.write(f'{xc}.bee')
e, de, contribs, seed, xc = readbee(f'{xc}.bee', all=True)
assert e + de == pytest.approx(energies, abs=1e-12)
e2000 = ensemble(e, contribs, xc)
assert e2000.shape == (2000, )
# From data:
ens = BEEFEnsemble(e=e, contribs=contribs, xc=xc, verbose=False)
energies2 = ens.get_ensemble_energies(size)
assert energies2 == pytest.approx(energies, abs=1e-12)
h2 = Atoms('H2', [[0, 0, 0], [0, 0, d]])
h2.center(vacuum=2)
h2.calc = GPAW(txt='H2-' + xc + '.txt', convergence=c)
h2.get_potential_energy()
h2.calc.set(xc=xc)
h2.get_potential_energy()
h2.get_forces()
ens = BEEFEnsemble(h2.calc)
e_h2 = ens.get_ensemble_energies()
# H atom:
h = Atoms('H', cell=h2.cell, magmoms=[1])
h.center()
h.calc = GPAW(txt='H-' + xc + '.txt', convergence=c)
h.get_potential_energy()
h.calc.set(xc=xc)
h.get_potential_energy()
ens = BEEFEnsemble(h.calc)
e_h = ens.get_ensemble_energies()
# binding energy
ae = 2 * e_h - e_h2
print(ae.mean(), ae.std())
equal(ae.mean(), E0, 0.015)
equal(ae.std(), dE0, 0.015)
ens.write('H')
world.barrier()
energies = readbee('H')
equal(abs(energies - e_h).max(), 0, 1e-12)
# Does not work with libxc-4
continue
E = []
V = []
for a in np.linspace(5.4, 5.5, 3):
si = bulk('Si', a=a)
si.calc = GPAW(txt='Si-' + xc + '.txt',
mixer=Mixer(0.8, 7, 50.0),
xc=xc,
kpts=[2, 2, 2],
mode=PW(200))
E.append(si.get_potential_energy())
ens = BEEFEnsemble(si.calc, verbose=False)
ens.get_ensemble_energies(200)
ens.write('Si-{}-{:.3f}'.format(xc, a))
V.append(si.get_volume())
p = np.polyfit(V, E, 2)
v0 = np.roots(np.polyder(p))[0]
a = (v0 * 4)**(1 / 3)
a0, da0 = results[xc]
assert abs(a - a0) < 0.001, (xc, a, a0)
if world.rank == 0:
E = []
for a in np.linspace(5.4, 5.5, 3):
e = readbee('Si-{}-{:.3f}'.format(xc, a))
E.append(e)
h2 = Atoms("H2", [[0, 0, 0], [0, 0, d]])
h2.center(vacuum=2)
h2.calc = GPAW(txt="H2-" + xc + ".txt", convergence=c)
h2.get_potential_energy()
h2.calc.set(xc=xc)
h2.get_potential_energy()
h2.get_forces()
ens = BEEFEnsemble(h2.calc)
e_h2 = ens.get_ensemble_energies()
# H atom:
h = Atoms("H", cell=h2.cell, magmoms=[1])
h.center()
h.calc = GPAW(txt="H-" + xc + ".txt", convergence=c)
h.get_potential_energy()
h.calc.set(xc=xc)
h.get_potential_energy()
ens = BEEFEnsemble(h.calc)
e_h = ens.get_ensemble_energies()
# binding energy
ae = 2 * e_h - e_h2
print(ae.mean(), ae.std())
equal(ae.mean(), E0, 0.015)
equal(ae.std(), dE0, 0.015)
ens.write("H")
world.barrier()
energies = readbee("H")
equal(abs(energies - e_h).max(), 0, 1e-12)