Dear Pamela
Let me paste again here a recent little guide I've posted a few weeks
ago in the forum:
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 standard "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}
My 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 (taken from some measured reference)
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 example 2))
experimental unresolved N1+N3 line = 406.8 eV
HTH, but write me in private if something is not clear.
Giuseppe
Quoting Pamela Svensson <[email protected]>:
I am computing the Binding energies for some C 1s core levels in a
molecule, to be compared to an XPS experiment. My problem is related
to the core level shift and the ordering of the computed energies
(we are not worrying for the absolute values of course but for the
relative values).
According to the experiment we have one C 1s XPS peak at 291 eV
(Carbon 1) and three very close to each other at about 290 eV
(Carbon 2 3 and 4). (in the experiment they express the Binding
Energy (BE) as positive, meaning the C1 1s core electron has
stronger BE than C2 1s in our case).
The total energies computed for our molecule with quantum espresso
with a full core hole in the various carbon atoms are:
core hole in C1 1s= - 263.84140093 Ry (higher)
core hole in C2, 3 and 4 1s ~ -263.89 Ry (lower)
and the ground state (GS) energy for the system is -246.5 Ry (even higher)
(I would expect the GS energy to be lower than the energy of the
system with the core hole since I have extracted one electron, but
maybe this is only true for a full electron calculation?)
Since we know from the experimental XPS that the binding energy of
C1 1s core level is higher than that of C2 1s, why do we get a lower
total energy when we perform a core hole in C2 1s than in C1 1s?
In addition, the difference between the GS energy and the total
energy with the core hole on C1s is lower than for the core hole in
C2, 3 and 4, which is the opposite of what happens in the experiment.
We wonder how we should interpret these total energies in relation
to the experimental XPS, and if these total energies we obtain make
sense.
Thank you very much!
Pamela Svensson
Uppsala University
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GIUSEPPE MATTIOLI
CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
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E-mail: <[email protected]>
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