def calculator():
# Obviously this calculator should be adapted
return SJM(
poissonsolver={'dipolelayer': 'xy'},
gpts=(48, 32, 168),
kpts=(4, 6, 1),
xc='PBE',
spinpol=False,
potential=potential,
occupations=FermiDirac(0.1),
maxiter=400,
cavity=EffectivePotentialCavity(
effective_potential=SJMPower12Potential(atomic_radii,
u0,
H2O_layer=True),
temperature=T,
surface_calculator=GradientSurface()),
dielectric=LinearDielectric(epsinf=epsinf),
interactions=[SurfaceInteraction(surface_tension=gamma)],
)
solvent.calc = calc
solvent.get_potential_energy() #converge WFs with PBE
calc.set(xc=beef)
solvent.calc = calc
E_sv = solvent.get_potential_energy() #BEEF best fit energy
ense = BEEFEnsemble(calc)
dE_sv = ense.get_ensemble_energies(
) #N=2000 non-self-consist calculation to generate uncertainty spread
#Perform solvent-only (solvated phase) calculation
scalc = SolvationGPAW(xc=xc,
gpts=h2gpts(h, solvent.get_cell(), idiv=16),
cavity=EffectivePotentialCavity(
effective_potential=Power12Potential(
atomic_radii, u0),
temperature=T,
surface_calculator=GradientSurface()),
dielectric=LinearDielectric(epsinf=epsinf),
interactions=[SurfaceInteraction(surface_tension=gamma)])
solvent.calc = scalc
solvent.get_potential_energy()
scalc.set(xc=beef)
solvent.calc = scalc
E_sv_sol = solvent.get_potential_energy()
ense = BEEFEnsemble(scalc)
dE_sv_sol = ense.get_ensemble_energies()
'''
#Perform single-ion (gas phase) calculation
ion = Atoms(sym)
T = 298.15
vdw_radii = vdw_radii.copy()
vdw_radii[1] = 1.09
atomic_radii = lambda atoms: [vdw_radii[n] for n in atoms.numbers]
convergence = {
'energy': 0.05 / 8.,
'density': 10.,
'eigenstates': 10.,
}
atoms = Cluster(molecule('H2O'))
atoms.minimal_box(vac, h)
atoms.pbc = True
with warnings.catch_warnings():
# ignore production code warning for ADM12PoissonSolver
warnings.simplefilter("ignore")
psolver = ADM12PoissonSolver(eps=1e-7)
atoms.calc = SolvationGPAW(
xc='LDA', h=h, convergence=convergence,
cavity=EffectivePotentialCavity(
effective_potential=Power12Potential(atomic_radii=atomic_radii, u0=u0),
temperature=T
),
dielectric=LinearDielectric(epsinf=epsinf),
poissonsolver=psolver
)
atoms.get_potential_energy()
atoms.get_forces()
def print_results(atoms):
parprint('E = %.3f eV' % (atoms.get_potential_energy(), ))
parprint('V = %.3f Ang ** 3' % (atoms.calc.get_cavity_volume(), ))
parprint('A = %.3f Ang ** 2' % (atoms.calc.get_cavity_surface(), ))
parprint('Forces:')
parprint(atoms.get_forces())
parprint('')
# Cavity from 1 / r ** 12 effective potential
atoms.calc = SolvationGPAW(
xc=xc,
h=h,
cavity=EffectivePotentialCavity(
effective_potential=Power12Potential(atomic_radii=atomic_radii, u0=u0),
temperature=T,
surface_calculator=GradientSurface(),
volume_calculator=KB51Volume(compressibility=kappa_T, temperature=T)),
dielectric=LinearDielectric(epsinf=epsinf),
interactions=[
SurfaceInteraction(surface_tension=gamma),
VolumeInteraction(pressure=p),
LeakedDensityInteraction(voltage=V_leak)
])
print_results(atoms)
# Cavity from electron density a la ADM12
atoms.calc = SolvationGPAW(xc=xc,
h=h,
poissonsolver=ADM12PoissonSolver(),
cavity=ADM12SmoothStepCavity(