Calculation of XPS absolute BE on surface slab

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Calculation of XPS absolute BE on surface slab

Date: 2025/01/23 22:34
Name: Harry <harry@cp.prec.eng.osaka-u.ac.jp>: Dear OpenMX developers,

Thank you very much for the developing the feature to calculate absolute Binding Energy.
I'm interested in applying this method for the case of adsorbates.
However, upon trying to calculate simple adsorption system, I could not reproduce the experimental XPS binding energy.

I took ethylene (C2H4) as an example.

I can reproduce the experimental XPS BE of ethylene (i.e., ~290.5 eV).

However, when putting it on the slab, the I got the XPS BE of ~283.6 eV, while the experimental value is ~285.0 eV. (https://doi.org/10.1016/0039-6028(80)90096-5).
The calculation using Gaussian Augmented Plane Wave method (GAPW) with no pseudopotentials can reproduce the experimental value.

The OpenMX calculation gave me BE of 283.6 eV.
Since I could not find example in the tutorial about the application on the slab,
I wonder whether the discrepancy is due to error in the input file, or the limitation of the theory itself.

Basically I used the same parameters as for the bulk case.
That is, the total charge equals to 0.0, and the Coulomb cutoff is on.
I wonder is there additional settings that I should consider?

I also noticed that the application in this paper (https://pubs.rsc.org/en/content/articlelanding/2025/cp/d4cp03942d) sets off the Coulomb cutoff. I'd like to ask what is the reason?

Thank you very much for your kind attention..
I'd really appreciate any comments on this matter.

Below is my input files if necessary.

#
# init file
#

System.CurrrentDirectory ./ # default=./
System.Name init
level.of.stdout 1 # default=1 (1-3)
level.of.fileout 0 # default=1 (0-2)

#
#
# Definition of Atomic Species
#

Species.Number 4
<Definition.of.Atomic.Species
H H7.0-s3p2 H_PBE19
C C7.0_1s-s4p3d2 C_PBE19_1s
C1 C7.0_1s_CH-s4p3d2 C_PBE19_1s
Ag Ag7.0-s3p2d1 Ag_PBE19
Definition.of.Atomic.Species>

#
# Atoms
#

Atoms.Number 42
Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU
<Atoms.SpeciesAndCoordinates
1 Ag 2.17504826 0.4181958 10.51050015 8.5 8.5
2 Ag 3.61443487 1.24922595 12.8610087 8.5 8.5
3 Ag 2.1847975 2.0846091 15.22183196 8.5 8.5
4 Ag 2.1704108 0.40847184 17.56997875 8.5 8.5
5 Ag 3.61443487 2.91128538 10.51050015 8.5 8.5
6 Ag 5.05382148 3.74231553 12.8610087 8.5 8.5
7 Ag 3.61461695 4.56327342 15.22163564 8.5 8.5
8 Ag 3.61083704 2.9122461 17.66123043 8.5 8.5
9 Ag 5.05382149 5.40437497 10.51050015 8.5 8.5
10 Ag 6.4932081 6.23540512 12.8610087 8.5 8.5
11 Ag 5.05026011 7.06910105 15.18820222 8.5 8.5
12 Ag 5.05969087 5.41374991 17.56593474 8.5 8.5
13 Ag 5.05382149 0.4181958 10.51050015 8.5 8.5
14 Ag 6.4932081 1.24922595 12.8610087 8.5 8.5
15 Ag 5.0439824 2.08507219 15.22373828 8.5 8.5
16 Ag 5.05687349 0.41134245 17.57399044 8.5 8.5
17 Ag 6.4932081 2.91128538 10.51050015 8.5 8.5
18 Ag 7.93259471 3.74231553 12.8610087 8.5 8.5
19 Ag 6.49583413 4.57474844 15.19748684 8.5 8.5
20 Ag 6.49990008 2.91227348 17.56717917 8.5 8.5
21 Ag 7.93259471 5.40437497 10.51050015 8.5 8.5
22 Ag 9.37198132 6.23540512 12.8610087 8.5 8.5
23 Ag 7.93294832 7.06463315 15.19877475 8.5 8.5
24 Ag 7.93202252 5.40544022 17.59516993 8.5 8.5
25 Ag 7.93259471 0.4181958 10.51050015 8.5 8.5
26 Ag 9.37198132 1.24922595 12.8610087 8.5 8.5
27 Ag 7.93080674 2.07521952 15.186833 8.5 8.5
28 Ag 7.93208435 0.4180024 17.58887459 8.5 8.5
29 Ag 9.37198133 2.91128538 10.51050015 8.5 8.5
30 Ag 10.81136794 3.74231553 12.8610087 8.5 8.5
31 Ag 9.36909845 4.57552956 15.19575257 8.5 8.5
32 Ag 9.35803299 2.91210598 17.5562551 8.5 8.5
33 Ag 10.81136794 5.40437497 10.51050015 8.5 8.5
34 Ag 12.25075455 6.23540512 12.8610087 8.5 8.5
35 Ag 10.81420449 7.07048264 15.18728157 8.5 8.5
36 Ag 10.80405238 5.4169595 17.56041705 8.5 8.5
37 C 2.83394927 3.0065905 20.4437531 3.0 3.0
38 C 4.17738354 3.00619476 20.46729574 3.0 3.0
39 H 2.25603561 2.0778695 20.49715941 0.5 0.5
40 H 2.25924622 3.93750017 20.40059349 0.5 0.5
41 H 4.75278907 2.07794684 20.54086884 0.5 0.5
42 H 4.75227955 3.93788748 20.4436329 0.5 0.5
Atoms.SpeciesAndCoordinates>
Atoms.UnitVectors.Unit Ang # Ang|AU
<Atoms.UnitVectors
8.636319680770924 0.0 0.0
4.318159840385462 7.4792687515396405 0.0
0.0 0.0 31.051524686785264
Atoms.UnitVectors>

#
# SCF or Electronic System
#

scf.XcType GGA-PBE # LDA|LSDA-CA|LSDA-PW|GGA-PBE
scf.SpinPolarization on # On|Off|NC
scf.SpinOrbit.Coupling off # On|Off, default=off
scf.ElectronicTemperature 300.0 # default=300 (K)
scf.energycutoff 360.0 # default=150 (Ry)
#scf.Ngrid 150 150 150
scf.maxIter 100 # default=40
scf.EigenvalueSolver band # DC|GDC|Cluster|Band
scf.Kgrid 4 4 1 # means n1 x n2 x n3
scf.Mixing.Type rmm-diisk # Simple|Rmm-Diis|Gr-Pulay|Kerker|Rmm-Diisk
scf.Init.Mixing.Weight 0.10 # default=0.30
scf.Min.Mixing.Weight 0.001 # default=0.001
scf.Max.Mixing.Weight 0.200 # default=0.40
scf.Mixing.History 40 # default=5
scf.Mixing.StartPulay 10 # default=6
scf.Mixing.EveryPulay 1 # default=6
scf.criterion 1.0e-8 # default=1.0e-6 (Hartree)

data.path /home/issp/materiapps/PrgEnv-intel_8.3.3/openmx/openmx-3.9.9-1/DFT_DATA19/

# final file
#

System.CurrrentDirectory ./ # default=./
System.Name finalC1
level.of.stdout 1 # default=1 (1-3)
level.of.fileout 0 # default=1 (0-2)

#
#
# Definition of Atomic Species
#

Species.Number 4
<Definition.of.Atomic.Species
H H7.0-s3p2 H_PBE19
C C7.0_1s-s4p3d2 C_PBE19_1s
C1 C7.0_1s_CH-s4p3d2 C_PBE19_1s
Ag Ag7.0-s3p2d1 Ag_PBE19
Definition.of.Atomic.Species>

#
# Atoms
#

Atoms.Number 42
Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU
<Atoms.SpeciesAndCoordinates
1 Ag 2.17504826 0.4181958 10.51050015 8.5 8.5
2 Ag 3.61443487 1.24922595 12.8610087 8.5 8.5
3 Ag 2.1847975 2.0846091 15.22183196 8.5 8.5
4 Ag 2.1704108 0.40847184 17.56997875 8.5 8.5
5 Ag 3.61443487 2.91128538 10.51050015 8.5 8.5
6 Ag 5.05382148 3.74231553 12.8610087 8.5 8.5
7 Ag 3.61461695 4.56327342 15.22163564 8.5 8.5
8 Ag 3.61083704 2.9122461 17.66123043 8.5 8.5
9 Ag 5.05382149 5.40437497 10.51050015 8.5 8.5
10 Ag 6.4932081 6.23540512 12.8610087 8.5 8.5
11 Ag 5.05026011 7.06910105 15.18820222 8.5 8.5
12 Ag 5.05969087 5.41374991 17.56593474 8.5 8.5
13 Ag 5.05382149 0.4181958 10.51050015 8.5 8.5
14 Ag 6.4932081 1.24922595 12.8610087 8.5 8.5
15 Ag 5.0439824 2.08507219 15.22373828 8.5 8.5
16 Ag 5.05687349 0.41134245 17.57399044 8.5 8.5
17 Ag 6.4932081 2.91128538 10.51050015 8.5 8.5
18 Ag 7.93259471 3.74231553 12.8610087 8.5 8.5
19 Ag 6.49583413 4.57474844 15.19748684 8.5 8.5
20 Ag 6.49990008 2.91227348 17.56717917 8.5 8.5
21 Ag 7.93259471 5.40437497 10.51050015 8.5 8.5
22 Ag 9.37198132 6.23540512 12.8610087 8.5 8.5
23 Ag 7.93294832 7.06463315 15.19877475 8.5 8.5
24 Ag 7.93202252 5.40544022 17.59516993 8.5 8.5
25 Ag 7.93259471 0.4181958 10.51050015 8.5 8.5
26 Ag 9.37198132 1.24922595 12.8610087 8.5 8.5
27 Ag 7.93080674 2.07521952 15.186833 8.5 8.5
28 Ag 7.93208435 0.4180024 17.58887459 8.5 8.5
29 Ag 9.37198133 2.91128538 10.51050015 8.5 8.5
30 Ag 10.81136794 3.74231553 12.8610087 8.5 8.5
31 Ag 9.36909845 4.57552956 15.19575257 8.5 8.5
32 Ag 9.35803299 2.91210598 17.5562551 8.5 8.5
33 Ag 10.81136794 5.40437497 10.51050015 8.5 8.5
34 Ag 12.25075455 6.23540512 12.8610087 8.5 8.5
35 Ag 10.81420449 7.07048264 15.18728157 8.5 8.5
36 Ag 10.80405238 5.4169595 17.56041705 8.5 8.5
37 C 2.83394927 3.0065905 20.4437531 3.0 3.0
38 C1 4.17738354 3.00619476 20.46729574 3.0 3.0
39 H 2.25603561 2.0778695 20.49715941 0.5 0.5
40 H 2.25924622 3.93750017 20.40059349 0.5 0.5
41 H 4.75278907 2.07794684 20.54086884 0.5 0.5
42 H 4.75227955 3.93788748 20.4436329 0.5 0.5
Atoms.SpeciesAndCoordinates>
Atoms.UnitVectors.Unit Ang # Ang|AU
<Atoms.UnitVectors
8.636319680770924 0.0 0.0
4.318159840385462 7.4792687515396405 0.0
0.0 0.0 31.051524686785264
Atoms.UnitVectors>

#
# SCF or Electronic System
#

scf.restart on
scf.restart.filename init
scf.coulomb.cutoff on
scf.core.hole on

<core.hole.state
38 s 1
core.hole.state>

scf.system.charge 0.0 # default=0.0

scf.XcType GGA-PBE # LDA|LSDA-CA|LSDA-PW|GGA-PBE
scf.SpinPolarization on # On|Off|NC
scf.SpinOrbit.Coupling off # On|Off, default=off
scf.ElectronicTemperature 300.0 # default=300 (K)
scf.energycutoff 360.0 # default=150 (Ry)
#scf.Ngrid 150 150 150
scf.maxIter 100 # default=40
scf.EigenvalueSolver band # DC|GDC|Cluster|Band
scf.Kgrid 4 4 1 # means n1 x n2 x n3
scf.Mixing.Type rmm-diisk # Simple|Rmm-Diis|Gr-Pulay|Kerker|Rmm-Diisk
scf.Init.Mixing.Weight 0.10 # default=0.30
scf.Min.Mixing.Weight 0.001 # default=0.001
scf.Max.Mixing.Weight 0.200 # default=0.40
scf.Mixing.History 40 # default=5
scf.Mixing.StartPulay 10 # default=6
scf.Mixing.EveryPulay 1 # default=6
scf.criterion 1.0e-8 # default=1.0e-6 (Hartree)

data.path /home/issp/materiapps/PrgEnv-intel_8.3.3/openmx/openmx-3.9.9-1/DFT_DATA19/

Page: [1]

Re: Calculation of XPS absolute BE on surface slab ( No.1 )

Date: 2025/01/30 21:24
Name: T. Ozaki

Hi,

For the final state calculation, there are two ways:

One is to treat the system as insulator for which the parameters can be set as

scf.restart on
scf.restart.filename init
scf.coulomb.cutoff on
scf.core.hole on

<core.hole.state
38 s 1
core.hole.state>

scf.system.charge 1.0 # default=0.0

The system charge needs to be set 1.0 rather than 0.0.

The second way is to treat the system as metal for which the parameters can be set as

scf.restart off
scf.restart.filename init
scf.coulomb.cutoff off
scf.core.hole on

<core.hole.state
38 s 1
core.hole.state>

scf.system.charge 0.0 # default=0.0

Could you try both of them, and report the results?

Regards,

TO

Re: Calculation of XPS absolute BE on surface slab ( No.2 )

Date: 2025/02/05 15:53
Name: Harry <harry@cp.prec.eng.osaka-u.ac.jp>

Dear Prof. Ozaki,

Thank you for kind reply.
I'm sorry I don't notice the reply on this forum sooner.

Below is the result of my calculation:

************ Assuming the insulator case ******************
init.out: Enpy. -4186.020932596960 Ha
finalC1.out: Enpy. -4175.415962204526 Ha

The chemical potential in init.out: -0.14713639562808 Ha

The BE: final - init + mu = 284.57 eV.

************ Assuming the metal case ******************
init.out: Enpy. -4186.020000858669
finalC1.out: Enpy. -4175.589606084631

The BE: final - init = 283.82 eV

The insulator treatment gives better agreement with experiment of 285.0 eV.
I have tried to change the basis set, change the cutoff energy, change the size of unit cell but the result does not change so much.

I think I should put +1.0 charge to my system.
I would appreciate if you have any comment or suggestion.
Thank you again for your suggestion.

With best regards,

Harry

Re: Calculation of XPS absolute BE on surface slab ( No.3 )

Date: 2025/02/05 21:34
Name: T. Ozaki

Hi,

It should be noted that the calculated binding energies do not always exhibit good agreement with the experimental values.
As shown in https://www.openmx-square.org/vps_pao_core2019/B/index.html
large deviation can be seen in some cases. Also, a variation can be found even in experimental values.
Rather than being elated or discouraged by the agreement of individual data, it would be better to assess
the data as a whole, while keeping the computational condition.

Regards,

TO

Re: Calculation of XPS absolute BE on surface slab ( No.4 )

Date: 2025/02/06 17:58
Name: Harry <harry@cp.prec.eng.osaka-u.ac.jp>

Dear Prof. Ozaki,

Thank you for the reply.
I understand your points.
Then I will proceed with my calculations.

Thank you again for your help.

Best regards,

Harry

Page: [1]