[QE-users] Negative Core Electron Binding Energy
Giuseppe Mattioli
giuseppe.mattioli at ism.cnr.it
Wed Jan 15 14:16:08 CET 2020
Dear Carlos
Calculation of XPS lines are tricky. First of all you are not
simulating a real ionization process, but the reaction of the ground
state valence electrons of your system to the change of
pseudopotential. The related Delta_scf energy can be used to estimate
the XPS chemical shift, often with an impressive accuracy in my
experience with molecules (please, see J. Phys. Chem. A 2009, 113,
13593; RSC Adv. 2014, 4, 5272; Phys. Chem. Chem. Phys. 2018, 20,
6657), but in itself it has no meaning. It must be referenced to the
known value of something. I generally include a small molecule in the
same supercell, not interacting with the system; this is possible only
if you are computing isolated systems or surfaces. Best results for
molecules are obtained by using the B3LYP functional. For example, in
the case of a single uracil molecule, after the "relax" calculation
you have to:
1) "ionize" the reference with the core-hole pseudopotential
&control
calculation = 'scf'
/
&system
ibrav=1, celldm(1)=40.0000,
nat=16, ntyp=5, tot_charge=+1.0, <--- please NOTE THIS!
ecutwfc=90.0,
ecutfock=90.0,
nspin=1,
input_dft='b3lyp'
vdw_corr='grimme-d3',
/
&electrons
diagonalization='david',
mixing_mode='plain',
mixing_beta=0.1,
conv_thr=1.0d-7,
electron_maxstep=100
scf_must_converge=.false.,
adaptive_thr=.true.
/
&ions
ion_dynamics='bfgs'
/
ATOMIC_SPECIES
O 15.999 O.blyp-mt.UPF
N 14.007 N.blyp-mt.UPF
C 12.011 C.blyp-mt.UPF
H 1.008 H.blyp-vbc.UPF
F 14.007 N.blyp-mt-1sstar-gipaw-gm.UPF <-- F is to avoid that
dft-d3 complains
ATOMIC_POSITIONS {angstrom}
O 8.935874112 10.808337666 10.583540000
O 11.039204698 6.744187277 10.583540000
N 9.960179856 8.771477479 10.583540000
N 8.750099382 6.798630762 10.583540000
C 7.576844535 7.514397937 10.583540000
C 7.561763507 8.857734355 10.583540000
C 8.815185907 9.596007009 10.583540000
C 10.009803757 7.390627750 10.583540000
H 6.641921924 9.414782335 10.583540000
H 6.675458991 6.922669854 10.583540000
H 10.852028379 9.243449902 10.583540000
H 8.749194951 5.793547675 10.583540000
F 0.000000000 0.000000000 0.000000000
H 0.929248650 -0.004393660 -0.399583280
H -0.481589560 0.814895350 -0.356607030
H -0.484872120 -0.817298880 -0.346525310
K_POINTS {gamma}
2) "ionize" the desired atom(s) with the core-hole pseudopotential
&control
calculation = 'scf'
/
&system
ibrav=1, celldm(1)=40.0000,
nat=16, ntyp=5, tot_charge=+1.0,
ecutwfc=90.0,
ecutfock=90.0,
nspin=1,
input_dft='b3lyp'
vdw_corr='grimme-d3',
/
&electrons
diagonalization='david',
mixing_mode='plain',
mixing_beta=0.1,
conv_thr=1.0d-7,
electron_maxstep=100
scf_must_converge=.false.,
adaptive_thr=.true.
/
ATOMIC_SPECIES
O 15.999 O.blyp-mt.UPF
N 14.007 N.blyp-mt.UPF
C 12.011 C.blyp-mt.UPF
H 1.008 H.blyp-vbc.UPF
F 14.007 N.blyp-mt-1sstar-gipaw-gm.UPF
ATOMIC_POSITIONS {angstrom}
O 8.935874112 10.808337666 10.583540000 1 1 0
O 11.039204698 6.744187277 10.583540000 1 1 0
F 9.960179856 8.771477479 10.583540000 1 1 0
N 8.750099382 6.798630762 10.583540000 1 1 0
C 7.576844535 7.514397937 10.583540000 1 1 0
C 7.561763507 8.857734355 10.583540000 1 1 0
C 8.815185907 9.596007009 10.583540000 1 1 0
C 10.009803757 7.390627750 10.583540000 1 1 0
H 6.641921924 9.414782335 10.583540000 1 1 0
H 6.675458991 6.922669854 10.583540000 1 1 0
H 10.852028379 9.243449902 10.583540000 1 1 0
H 8.749194951 5.793547675 10.583540000 1 1 0
N 0.000000000 0.000000000 0.000000000 0 0 0
H 0.929248650 -0.004393660 -0.399583280
H -0.481589560 0.814895350 -0.356607030
H -0.484872120 -0.817298880 -0.346525310
K_POINTS {gamma}
The results are
1) -188.25465790 Ry (NH3 core hole)
2) -188.18332891 Ry (uracil N1 core hole)
E2-E1= 0.97 eV
NH3 N 1s = 405.60 eV (measured)
uracil N1 N 1s = 406.57 eV
uracil N3 N 1s = 407.00 eV (to obtain this you must change the
position of the "F" atom in 2))
experimental unresolved N1+N3 line = 406.8 eV
HTH, but write me in private if something is not clear.
Giuseppe
Quoting "Ayestaran Latorre, Carlos"
<carlos.ayestaran-latorre17 at imperial.ac.uk>:
> Dear QE users,
>
> I am trying to calculate binding energy shifts of N 1s core
> electrons for comparison with XPS spectra for nitrogen-containing
> system. For that purpose, I am using two PPs from the QE library:
> N.pbe-n-rrkjus_psl.1.0.0.UPF and the corresponding 1s core-hole one
> N.star1s-pbe-rrkjus.UPF.
>
> The standard procedure involves calculating the energy of a system
> with N electrons and comparing with the equivalent system with N-1
> electrons, achieved by using the core hole PP, so that a simple
> definition of binding energy (energy required to remove the
> electron) might be BE=E(N-1)-E(N). The problem I am having is that I
> am getting negative values, I suspect due to some simple error I
> have overlooked.
>
> As an example, I attach the input for a N2 molecule, relaxed without
> core-hole, and that now includes a core-hole in one of the atoms.
> The binding energy predicted by this configuration is (rounding
> numbers):
>
> BE=E(N-1)-E(N)=-51.47Ry-(-40.87Ry)=-10.62 Ry=-144.53 eV
>
> So even if the sign was flipped the absolute value is very far from
> the ~400eV of the N1s XPS peak. Any help is appreciated.
>
> Kind regards,
>
> Carlos Ayestarán Latorre
>
> PhD student
> Department of Mechanical Engineering
> Imperial College London
GIUSEPPE MATTIOLI
CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
Via Salaria Km 29,300 - C.P. 10
I-00015 - Monterotondo Scalo (RM)
Mob (*preferred*) +39 373 7305625
Tel + 39 06 90672342 - Fax +39 06 90672316
E-mail: <giuseppe.mattioli at ism.cnr.it>
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