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import numpy as np
import pytest
from ase.build import molecule
@pytest.fixture()
def atoms():
atoms = molecule('H2')
atoms.positions -= atoms.positions[0]
assert atoms.positions[0] == pytest.approx([0, 0, 0])
atoms.pbc = 1
atoms.cell = [5, 5, 6]
return atoms
k_ref_0 = 40.0 # Arbitrary "default" reference value
# Spring constant of H-H bond
k_refs = dict(
abinit=46,
cp2k=44,
espresso=43,
gpaw=39,
mopac=66,
nwchem=42,
siesta=45,
)
calc = pytest.mark.calculator
@calc('abinit', chksymtnons=0)
@calc('cp2k')
@calc('espresso', input_data={"control": {"tprnfor": True}})
@calc('gpaw', mode='pw', symmetry='off', txt=None)
@calc('mopac', method='PM7', task='1SCF UHF GRADIENTS')
@calc('nwchem')
@calc('siesta')
def test_h2_bond(factory, atoms):
d0 = atoms.get_distance(0, 1)
atoms.calc = factory.calc()
X = d0 + np.linspace(-0.08, 0.08, 5)
E = []
F = []
for x in X:
atoms.positions[1, 2] = x
e = atoms.get_potential_energy(force_consistent=True)
f = atoms.get_forces()
E.append(e)
F.append(f[1, 2])
E = np.array(E)
F = np.array(F)
a, b, _c = np.polyfit(X, E, 2)
xmin = -b / (2.0 * a)
fa, _fb = np.polyfit(X, F, 1)
k_from_energy = 2 * a
k_from_forces = -fa
# Not very strict for a bond length, but parameters are not consistent:
assert xmin == pytest.approx(0.77, rel=0.05)
assert k_from_energy == pytest.approx(k_from_forces, rel=0.05)
assert k_from_energy == pytest.approx(k_refs.get(factory.name, k_ref_0),
rel=0.05)
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