slab = fcc111('Pt', size=(1, 2, 3), orthogonal=True)
add_adsorbate(slab, 'C', 2.0, 'ontop')
add_adsorbate(slab, 'O', 3.15, 'ontop')
slab.center(axis=2, vacuum=4.0)
view(slab)
molecule = slab.copy()
del molecule[:-2]
# Molecule
molecule.set_calculator(c_mol)
molecule.get_potential_energy()
# H**o wavefunction
wf_u = [kpt.psit_nG[4] for kpt in c_mol.wfs.kpt_u]
# H**o projector overlaps
mol = range(len(slab))[-2:]
p_uai = [
dict([(mol[a], P_ni[4]) for a, P_ni in kpt.P_ani.items()])
for kpt in c_mol.wfs.kpt_u
]
# Slab with adsorbed molecule
slab.set_calculator(calc)
orbital = dscf.AEOrbital(calc, wf_u, p_uai, Estart=-100.0, Eend=0.0)
dscf.dscf_calculation(calc, [[-1.0, orbital, 1]], slab)
slab.get_potential_energy()
for k in range(len(c_mol.wfs.weight_k))]
wf2_k = [c_mol.get_pseudo_wave_function(band=6, kpt=k, spin=1)
for k in range(len(c_mol.wfs.weight_k))]
band_k = []
for k in range(len(c_mol.wfs.weight_k)):
wf1 = reshape(wf1_k[k], -1)
wf2 = reshape(wf2_k[k], -1)
p1 = abs(dot(wf1, lumo))
p2 = abs(dot(wf2, lumo))
if p1 > p2:
band_k.append(5)
else:
band_k.append(6)
#Lumo wavefunction
wf_u = [kpt.psit_nG[band_k[kpt.k]] for kpt in c_mol.wfs.kpt_u]
#Lumo projector overlaps
mol = range(len(slab))[-2:]
p_uai = [dict([(mol[a], P_ni[band_k[kpt.k]]) for a, P_ni in kpt.P_ani.items()])
for kpt in c_mol.wfs.kpt_u]
# Slab with adsorbed molecule
#-----------------------------------
slab.set_calculator(calc)
orbital = dscf.AEOrbital(calc, wf_u, p_uai)
dscf.dscf_calculation(calc, [[1.0, orbital, 1]], slab)
slab.get_potential_energy()
# state which is to be occupied. n=5,6 is the 2pix and 2piy orbitals
n = 5
molecule = [0, 1]
wf_u = [kpt.psit_nG[n].copy() for kpt in calc.wfs.kpt_u]
p_uai = [
dict([(molecule[a], P_ni[n].copy())
for a, P_ni in kpt.P_ani.items()]) for kpt in calc.wfs.kpt_u
]
#calc = GPAW(h=0.2, nbands=10, xc='PBE', spinpol=True,
# convergence={'bands': -2, 'eigenstates': 1.0e-9},
# occupations=FermiDirac(0.1), txt=name + '_es.txt')
#atoms.set_calculator(calc)
lumo = AEOrbital(calc, wf_u, p_uai)
dscf_calculation(calc, [[1.0, lumo, 1]], atoms)
e2 = atoms.get_potential_energy()
if world.rank == 0:
print('e1:', e1, 'e2:', e2, 'de:', e2 - e1)
calc.write(name + '_es.gpw', mode='all')
del wf_u, p_uai, lumo, calc, atoms
time.sleep(10)
while not os.path.isfile(name + '_es.gpw'):
print('Node %d waiting for %s...' % (world.rank, name + '_es.gpw'))
time.sleep(10)
world.barrier()
if not os.path.isfile(name + '_esx.gpw'):
calc = GPAW(name + '_es.gpw',
txt=name + '_esx.txt',
molecule = [0,1]
wf_u = [kpt.psit_nG[n] for kpt in calc_mol.wfs.kpt_u]
p_uai = [dict([(molecule[a], P_ni[n]) for a, P_ni in kpt.P_ani.items()])
for kpt in calc_mol.wfs.kpt_u]
# Excited state calculations
#--------------------------------------------
calc_1 = GPAW(nbands=8, h=0.2, xc='PBE', spinpol=True,
convergence={'energy': 100,
'density': 100,
#'eigenstates': 1.0e-9,
'bands': -1})
CO.set_calculator(calc_1)
weights = {0: [0.,0.,0.,1.], 1: [0.,0.,0.,-1.]}
lumo = dscf.MolecularOrbital(calc_1, weights=weights)
dscf.dscf_calculation(calc_1, [[1.0, lumo, 1]], CO)
E_es1 = CO.get_potential_energy()
niter_es1 = calc_1.get_number_of_iterations()
calc_1.write('dscf_CO_es1.gpw', mode='all')
calc_2 = GPAW(nbands=8, h=0.2, xc='PBE', spinpol=True,
convergence={'energy': 100,
'density': 100,
#'eigenstates': 1.0e-9,
'bands': -1})
CO.set_calculator(calc_2)
lumo = dscf.AEOrbital(calc_2, wf_u, p_uai)
dscf.dscf_calculation(calc_2, [[1.0, lumo, 1]], CO)
E_es2 = CO.get_potential_energy()
niter_es2 = calc_2.get_number_of_iterations()
calc_2.write('dscf_CO_es2.gpw', mode='all')
'density': 100,
'eigenstates': 1.0e-9,
'bands': -1
})
n = 5 # LUMO
molecule = [0, 1]
wf_u = [kpt.psit_nG[n] for kpt in calc_gs.wfs.kpt_u]
p_uai = [
dict([(molecule[a], P_ni[n]) for a, P_ni in kpt.P_ani.items()])
for kpt in calc_gs.wfs.kpt_u
]
atoms.set_calculator(calc_es)
lumo = dscf.AEOrbital(calc_es, wf_u, p_uai)
dscf.dscf_calculation(calc_es, [[1.0, lumo, 1]], atoms)
E1.append(atoms.get_potential_energy())
if i == 1:
F1 = atoms.get_forces()
f0 = np.sqrt(((F0[1, :] - F0[0, :])**2).sum()) * 0.5
f0b = (E0[1] - E0[0]) / delta # backward gradient
f0f = (E0[2] - E0[1]) / delta # forward gradient
if rank == 0:
print('Ground state')
print(E0)
print(f0b, '<', f0, '<', f0f)
assert f0 > f0b
assert f0 < f0f
txt = None,
mixer = MixerSum(beta=0.1, nmaxold=5, weight=50.0),
convergence = {'energy': 100,
'density': 100,
'eigenstates': 1.0e-9,
'bands': -1})
n = 5 # LUMO
molecule = [0, 1]
wf_u = [kpt.psit_nG[n] for kpt in calc_gs.wfs.kpt_u]
p_uai = [dict([(molecule[a], P_ni[n]) for a, P_ni in kpt.P_ani.items()])
for kpt in calc_gs.wfs.kpt_u]
atoms.set_calculator(calc_es)
lumo = dscf.AEOrbital(calc_es, wf_u, p_uai)
dscf.dscf_calculation(calc_es, [[1.0, lumo, 1]], atoms)
E1.append(atoms.get_potential_energy())
if i==1:
F1 = atoms.get_forces()
f0 = np.sqrt(((F0[1,:] - F0[0,:])**2).sum()) * 0.5
f0b = (E0[1] - E0[0]) / delta # backward gradient
f0f = (E0[2] - E0[1]) / delta # forward gradient
if rank == 0:
print 'Ground state'
print E0
print f0b, '<', f0, '<', f0f
assert f0 > f0b
assert f0 < f0f
# Obtain the pseudowavefunctions and projector overlaps of the
# state which is to be occupied. n=5,6 is the 2pix and 2piy orbitals
n = 5
molecule = [0, 1]
wf_u = [kpt.psit_nG[n].copy() for kpt in calc.wfs.kpt_u]
p_uai = [dict([(molecule[a], P_ni[n].copy()) for a, P_ni in
kpt.P_ani.items()]) for kpt in calc.wfs.kpt_u]
#calc = GPAW(h=0.2, nbands=10, xc='PBE', spinpol=True,
# convergence={'bands': -2, 'eigenstates': 1.0e-9},
# occupations=FermiDirac(0.1), txt=name + '_es.txt')
#atoms.set_calculator(calc)
lumo = AEOrbital(calc, wf_u, p_uai)
dscf_calculation(calc, [[1.0, lumo, 1]], atoms)
e2 = atoms.get_potential_energy()
if world.rank == 0:
print 'e1:', e1, 'e2:', e2, 'de:', e2-e1
calc.write(name + '_es.gpw', mode='all')
del wf_u, p_uai, lumo, calc, atoms
time.sleep(10)
while not os.path.isfile(name + '_es.gpw'):
print 'Node %d waiting for %s...' % (world.rank, name + '_es.gpw')
time.sleep(10)
world.barrier()
if not os.path.isfile(name + '_esx.gpw'):
calc = GPAW(name + '_es.gpw', txt=name + '_esx.txt', parallel={'band': 1})
calc.set_positions()