[QE-users] Adsorption calculation using Quantum ESPRESSO
Guru Ji
akhilg.nair at yahoo.in
Fri Aug 30 20:55:39 CEST 2024
The Cl is an isolated atom as these calculation involve chlorine in the
ground water which is mostly in the form of NaCl.
But in the literature, they have used an isolated Cl atom.
Is there a way to assign charge to atoms as the isolated atom should be in
the form of Cl-?
On Fri, Aug 30, 2024, 22:51 Giovanni Cantele <giovanni.cantele at spin.cnr.it>
wrote:
> 1) I would check the convergence of all calculations. In particular you
> use paw pseudos but ecutrhp = 4*ecutwfc. Values of 8 up to 12 times ecutwfc
> might be required
> 2) Did you calculate the energy of Cl as that of the isolated atom or as
> half that of the isolated Cl2 molecule that should be how Cl is found in
> gas form? What about this energy in your reference papers? Indeed, Cl2
> should result more stable thus giving to a larger formation energy in your
> formula
>
> Giovanni
>
> --
>
> Giovanni Cantele, PhD
> CNR-SPIN
> c/o Dipartimento di Fisica
> Universita' di Napoli "Federico II"
> Complesso Universitario M. S. Angelo - Ed. 6
> <https://www.google.com/maps/search/6+Via+Cintia,+I-80126,+Napoli,+Italy?entry=gmail&source=g>
> Via Cintia, I-80126, Napoli, Italy
> <https://www.google.com/maps/search/6+Via+Cintia,+I-80126,+Napoli,+Italy?entry=gmail&source=g>
> e-mail: giovanni.cantele at spin.cnr.it <giovanni.cantele at spin.cnr.it>
> Phone: +39 081 676910
> Skype contact: giocan74
>
> ResearcherID: http://www.researcherid.com/rid/A-1951-2009
> Web page: https://sites.google.com/view/giovanni-cantele/home
>
>
> Il giorno ven 30 ago 2024 alle 17:55 Akhil g.nair via users <
> users at lists.quantum-espresso.org> ha scritto:
>
>> Dear QE users,
>>
>> Following is the input to the adsorption of Cl on Cr2O3, where a slab is
>> created in the direction <001>:
>>
>> "
>> &CONTROL
>> calculation = "relax"
>> forc_conv_thr = 1.00000e-03
>> max_seconds = 8.64000e+05
>> nstep = 501
>> pseudo_dir = "."
>> /
>>
>> &SYSTEM
>> constrained_magnetization = "none"
>> degauss = 2.00000e-02
>> ecutrho = 360
>> ecutwfc = 90
>> ibrav = 0
>> nat = 121
>> nosym = .TRUE.
>> nspin = 1
>> ntyp = 3
>> occupations = "smearing"
>> smearing = "gaussian"
>>
>> /
>>
>> &ELECTRONS
>> conv_thr = 1.00000e-06
>> diago_david_ndim = 4
>> diagonalization = "david"
>> electron_maxstep = 501
>> mixing_beta = 1.00000e-01
>> mixing_mode = "plain"
>> mixing_ndim = 8
>> startingpot = "atomic"
>> startingwfc = "atomic+random"
>> /
>>
>> &IONS
>> ion_dynamics = "bfgs"
>> /
>>
>> &CELL
>> cell_dofree = "all"
>> cell_dynamics = "bfgs"
>> press = 0.00000e+00
>> press_conv_thr = 5.00000e-01
>> /
>>
>> K_POINTS {automatic}
>> 3 3 3 0 0 0
>>
>> CELL_PARAMETERS {angstrom}
>> 9.917520 0.000000 0.000000
>> -4.958760 8.588824 0.000000
>> 0.000000 0.000000 32.654000
>>
>> ATOMIC_SPECIES
>> Cr 51.99610 Cr.pbe-spn-kjpaw_psl.1.0.0.UPF
>> O 15.99940 O.pbe-n-kjpaw_psl.1.0.0.UPF
>> Cl 35.45270 Cl.pbe-n-kjpaw_psl.1.0.0.UPF
>>
>> ATOMIC_POSITIONS {crystal}
>> Cr 0.000000 0.000000 0.398385
>> Cr 0.500000 0.000000 0.398385
>> Cr 0.500000 0.500000 0.398385
>> Cr 0.000000 0.500000 0.398385
>> Cr 0.166667 0.333333 0.386590
>> Cr 0.666667 0.333333 0.386590
>> Cr 0.166667 0.833334 0.386590
>> Cr 0.666667 0.833334 0.386590
>> O 0.345700 0.000000 0.357795
>> O 0.845700 0.000000 0.357795
>> O 0.154300 0.154300 0.357795
>> O 0.654300 0.154300 0.357795
>> O 0.500000 0.345700 0.357795
>> O 0.000000 0.345700 0.357795
>> O 0.345700 0.500000 0.357795
>> O 0.845700 0.500000 0.357795
>> O 0.154300 0.654300 0.357795
>> O 0.654300 0.654300 0.357795
>> O 0.500000 0.845700 0.357795
>> O 1.000000 0.845700 0.357795
>> Cr 0.333333 0.166667 0.329000
>> Cr 0.833334 0.166667 0.329000
>> Cr 0.333333 0.666667 0.329000
>> Cr 0.833334 0.666667 0.329000
>> Cr 0.000000 0.000000 0.317204
>> Cr 0.500000 0.000000 0.317204
>> Cr 0.500000 0.500000 0.317204
>> Cr 0.000000 0.500000 0.317204
>> O 0.179033 0.012367 0.288409
>> O 0.679034 0.012367 0.288409
>> O 0.487633 0.166667 0.288409
>> O 0.987634 0.166667 0.288409
>> O 0.333333 0.320967 0.288409
>> O 0.833334 0.320967 0.288409
>> O 0.179033 0.512367 0.288409
>> O 0.679034 0.512367 0.288409
>> O 0.487633 0.666667 0.288409
>> O 0.987634 0.666667 0.288409
>> O 0.333333 0.820967 0.288409
>> O 0.833334 0.820967 0.288409
>> Cr 0.166667 0.333333 0.259614
>> Cr 0.666667 0.333333 0.259614
>> Cr 0.166667 0.833334 0.259614
>> Cr 0.666667 0.833334 0.259614
>> Cr 0.333333 0.166667 0.247819
>> Cr 0.833334 0.166667 0.247819
>> Cr 0.333333 0.666667 0.247819
>> Cr 0.833334 0.666667 0.247819
>> O 0.166667 0.179033 0.219024
>> O 0.666667 0.179033 0.219024
>> O 0.012367 0.333333 0.219024
>> O 0.512367 0.333333 0.219024
>> O 0.320967 0.487633 0.219024
>> O 0.820967 0.487633 0.219024
>> O 0.166667 0.679034 0.219024
>> O 0.666667 0.679034 0.219024
>> O 0.012367 0.833334 0.219024
>> O 0.512367 0.833334 0.219024
>> O 0.320967 0.987634 0.219024
>> O 0.820967 0.987634 0.219024
>> Cr 0.000000 0.000000 0.190229 0 0 0
>> Cr 0.500000 0.000000 0.190229 0 0 0
>> Cr 0.500000 0.500000 0.190229 0 0 0
>> Cr 0.000000 0.500000 0.190229 0 0 0
>> Cr 0.166667 0.333333 0.178433 0 0 0
>> Cr 0.666667 0.333333 0.178433 0 0 0
>> Cr 0.166667 0.833334 0.178433 0 0 0
>> Cr 0.666667 0.833334 0.178433 0 0 0
>> O 0.154300 0.000000 0.149638 0 0 0
>> O 0.654300 0.000000 0.149638 0 0 0
>> O 0.000000 0.154300 0.149638 0 0 0
>> O 0.500000 0.154300 0.149638 0 0 0
>> O 0.345700 0.345700 0.149638 0 0 0
>> O 0.845700 0.345700 0.149638 0 0 0
>> O 0.154300 0.500000 0.149638 0 0 0
>> O 0.654300 0.500000 0.149638 0 0 0
>> O 0.000000 0.654300 0.149638 0 0 0
>> O 0.500000 0.654300 0.149638 0 0 0
>> O 0.345700 0.845700 0.149638 0 0 0
>> O 0.845700 0.845700 0.149638 0 0 0
>> Cr 0.333333 0.166667 0.120843 0 0 0
>> Cr 0.833334 0.166667 0.120843 0 0 0
>> Cr 0.333333 0.666667 0.120843 0 0 0
>> Cr 0.833334 0.666667 0.120843 0 0 0
>> Cr 0.000000 0.000000 0.109048 0 0 0
>> Cr 0.500000 0.000000 0.109048 0 0 0
>> Cr 0.500000 0.500000 0.109048 0 0 0
>> Cr 0.000000 0.500000 0.109048 0 0 0
>> O 0.333333 0.012367 0.080253 0 0 0
>> O 0.833334 0.012367 0.080253 0 0 0
>> O 0.179033 0.166667 0.080253 0 0 0
>> O 0.679034 0.166667 0.080253 0 0 0
>> O 0.487633 0.320967 0.080253 0 0 0
>> O 0.987634 0.320967 0.080253 0 0 0
>> O 0.333333 0.512367 0.080253 0 0 0
>> O 0.833334 0.512367 0.080253 0 0 0
>> O 0.179033 0.666667 0.080253 0 0 0
>> O 0.679034 0.666667 0.080253 0 0 0
>> O 0.487633 0.820967 0.080253 0 0 0
>> O 0.987634 0.820967 0.080253 0 0 0
>> Cr 0.166667 0.333333 0.051458 0 0 0
>> Cr 0.666667 0.333333 0.051458 0 0 0
>> Cr 0.166667 0.833334 0.051458 0 0 0
>> Cr 0.666667 0.833334 0.051458 0 0 0
>> Cr 0.333333 0.166667 0.039662 0 0 0
>> Cr 0.833334 0.166667 0.039662 0 0 0
>> Cr 0.333333 0.666667 0.039662 0 0 0
>> Cr 0.833334 0.666667 0.039662 0 0 0
>> O 0.012367 0.179033 0.010868 0 0 0
>> O 0.512367 0.179033 0.010868 0 0 0
>> O 0.320967 0.333333 0.010868 0 0 0
>> O 0.820967 0.333333 0.010868 0 0 0
>> O 0.166667 0.487633 0.010868 0 0 0
>> O 0.666667 0.487633 0.010868 0 0 0
>> O 0.012367 0.679034 0.010868 0 0 0
>> O 0.512367 0.679034 0.010868 0 0 0
>> O 0.320967 0.833334 0.010868 0 0 0
>> O 0.820967 0.833334 0.010868 0 0 0
>> O 0.166667 0.987634 0.010868 0 0 0
>> O 0.666667 0.987634 0.010868 0 0 0
>> Cl 0.481508 0.500000 0.453947
>>
>> "
>>
>> *The last part of the output gives:*
>>
>> "
>> .
>> .
>> bfgs converged in 40 scf cycles and 39 bfgs steps
>> (criteria: energy < 1.0E-04 Ry, force < 1.0E-03 Ry/Bohr)
>>
>> End of BFGS Geometry Optimization
>>
>> Final energy = * -3808.8434290038* Ry
>>
>> "
>>
>> The same input after removing Cl, i.e., only Cr2O3, yields a final energy
>> of *-3729.3140139559 Ry*.
>>
>>
>> The same input with only Cl yields a final energy* of -79.2218317877 Ry.*
>>
>>
>> For calculating the adsorption energy of Cl on Cr2O3, the following
>> equation is used:
>>
>> *E(ads) = E(cr2o3+cl) − E (cr2o3) − E(cl)*
>>
>> This gives us the adsorption energy of Cl on Cr2O3 as *-0.31 Ry (i.e.,
>> -4.22 eV)*
>>
>>
>> However, if we look at the literature, this value normally lies in the *positive
>> region*, which is why Cr2O3 helps steel resist corrosion due to chlorine
>> attack.
>>
>> In my calculation, this value is coming negative. If anyone can guide me
>> in this regard, I will be really grateful.
>>
>> Regards
>>
>> Akhil Nair
>> Research scholar
>> HBNI, India.
>>
>>
>> On Friday 30 August, 2024 at 05:51:41 pm IST, Akhil g.nair <
>> akhilg.nair at yahoo.in> wrote:
>>
>>
>> Dear QE users,
>>
>> I was trying to calculate the adsorption energy of Cl on Cr2O3 using the
>> following methodology :
>> "Adsorption calcs using Quantum ESPRESSO
>> <https://mattermodeling.stackexchange.com/questions/9888/adsorption-calcs-using-quantum-espresso>
>> "
>>
>> Adsorption calcs using Quantum ESPRESSO
>>
>> I already built a copper surface using BURAI and I used an SCF
>> calculation to find the total energy of this surf...
>>
>> <https://mattermodeling.stackexchange.com/questions/9888/adsorption-calcs-using-quantum-espresso>
>>
>>
>> However, the values always come out to be negative. As per the literature
>> [Redirecting <https://doi.org/10.1016/j.actamat.2023.119477>], Cl
>> adsorption on Cr2O3 should have positive energy.
>>
>> Redirecting
>>
>> <https://doi.org/10.1016/j.actamat.2023.119477>
>>
>>
>> Currently, I am taking the 'Final Energy' at the end of the output file
>> from the QE calculation after the 'relax' calculation.
>>
>> Please let me know if I should consider any other values or if the
>> calculation methodology needs to be changed.
>>
>>
>> Regards
>>
>> Akhil Nair
>> Research scholar
>> HBNI, India
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>
>
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