def test_benzene_rpa():
coords, species, vol_ratios = benzene_dimer[0]
alpha_0, C6, R_vdw = from_volumes(species, vol_ratios)
ene = MBDGeom(coords, do_rpa=True).mbd_energy(
alpha_0, C6, R_vdw, 0.83, variant='plain'
)
assert ene == approx(-0.007002398506090302, rel=1e-9)
def test_mbd_coulomb():
a = 14.4
beta = 2.0
enes = []
for coords, species, vol_ratios in peptide_meoh:
geom = MBDGeom(coords, get_spectrum=True)
_, eigs, C = geom.mbd_energy_species(species, vol_ratios, beta=0.83)
omega_t = np.sqrt(eigs)
alpha_0, C6, R_vdw = from_volumes(species, vol_ratios)
omega = 4 * C6 / (3 * alpha_0 ** 2)
charges = np.ones_like(alpha_0)
masses = 1 / (alpha_0 * omega ** 2)
ecoul = geom.coulomb_energy(
charges, masses, omega_t, 'fermi', R_vdw, beta, a, C
)
edip = geom.dipole_energy(
alpha_0, omega, omega_t, 'fermi,dip', R_vdw, beta, a, C
)
C = np.identity(len(omega_t))
omega_non = np.repeat(omega, 3)
ecoul_non = geom.coulomb_energy(
charges, masses, omega_non, 'fermi', R_vdw, beta, a, C
)
edip_non = geom.dipole_energy(
alpha_0, omega, omega_t, 'fermi,dip', R_vdw, beta, a, C
)
enes.append(ecoul - edip - (ecoul_non - edip_non))
ene_int = enes[2] - enes[0] - enes[1]
assert ene_int == approx(0.0002460638172163822 / 627.503, rel=1e-10)
def _set_vdw_parameters(self, atoms=None):
#TODO: add functionality:
# . fractional ionic
# . RvdW from alpha
if hasattr(self, 'custom_beta'):
self.beta = self.custom_beta
else:
self.beta = beta_from_xc(self.xc)
self.alpha0_TS, self.C6_TS, self.RvdW_TS = \
from_volumes(atoms.get_chemical_symbols(), self.a_div_a0)