[QE-users] Negatively charged isolated molecule

Mon Mar 18 10:27:53 CET 2019

Dear QE-users,

I always thought that it is not correct to calculate energies of isolated ionic species under PBC due to the introduction of a Jellium background inside the vacuum  which has physically no meaning. But after reading this post I assume that I am wrong and that you can perform calculations on ionic species in a vacuum with QE?

With kind regards,
Laurens Siemons
PhD, UAntwerp (Belgium)
________________________________
Van: users <users-bounces at lists.quantum-espresso.org> namens Nattino Francesco <francesco.nattino at epfl.ch>
Verzonden: zaterdag 16 maart 2019 9:02
Aan: Quantum Espresso users Forum
Onderwerp: Re: [QE-users] Negatively charged isolated molecule

Dear Ernane,

 As Giuseppe already pointed out, many anionic species are actually unbound with standard density functionals. The continuum solvation model helps to achieve convergence because the dielectric embedding stabilizes the localized electronic configuration.

A way to circumvent the issue and to obtain the energy of carbonate in vacuum could be the following: you calculate the energy of the system for decreasing values of the dielectric constant and you extrapolate the energy to the vacuum dielectric constant (epsilon=1).

Best regards,

Francesco Nattino,
EPFL

On Mar 15, 2019 7:30 PM, Michal Krompiec <michal.krompiec at gmail.com> wrote:
Dear Ernane,
Have you thought of using a more sophisticated method (like GW) on [CO3]- to calculate its EA? This would give you the energy of [CO3]2- in vacuum.
Best,
Michal Krompiec
University of Southampton & Merck KGaA

On Fri, 15 Mar 2019 at 18:22, Ernane de Freitas Martins <ernanefmg at gmail.com<mailto:ernanefmg at gmail.com>> wrote:
Dear Giuseppe,

I really appreciate your answer. Thank you very much for using your time to answer my question.

I'll think on your suggestion about trying hybrid functionals. The point is that I need to estimate the solvation energy for carbonate ion using the environ module, then I'll need to run a vacuum calculation using the same functional I'm already using rVV-10).

Thank you again for replying.

Atenciosamente,

Dr. Ernane de Freitas Martins
Postdoctoral researcher
IF - USP
São Paulo, SP - Brazil

Em sex, 15 de mar de 2019 15:04, Giuseppe Mattioli <giuseppe.mattioli at ism.cnr.it<mailto:giuseppe.mattioli at ism.cnr.it>> escreveu:

Dear Ernane
Your question contains part of the answer! Carbonate ion (CO3 2-) is
not stable outside water, and calculations of its properties in gas
phase are likely not so meaningful, but in the case of model
thermodynamics cycles (e.g. Born-Haber). The excess negative charge is
unbound when not stabilized by a strongly polar solvent, and this is
likely responsible for instabilities in the construction of the
Kohn-Sham potential along scf iterations. Moreover, this happens on
top of the strong delocalization error you experience when you use a
standard GGA exchange-correlation functional, when the
self-interaction of strongly localized electrons in the J[n] Coulomb
potential is not cancelled by a same term in the semi local exchange
potential. You may minimize this latter source of error by using a
hybrid GGA-EXX functional such as B3LYP, where the non local
Hartree-Fock part of the exchange functional can recover part of the
delocalization error, but you are not free yet from the instability of
carbonate in gas phase.
HTH
Giuseppe

Ernane de Freitas Martins <ernanefmg at gmail.com<mailto:ernanefmg at gmail.com>> ha scritto:

> Hello,
>
> I'm experiencing a problem to run a negatively charge molecule in quantum
> espresso. The system is CO32-.
>
> I try both vacuum and solvated (environ) calculations. The solvated one
> works fine.
>
> The problem is the calculation in vacuum. It never give the first ionic
> step because the SCF accuracy never reaches the convence criterion.
>
> I tried many different solutions (increase cutoffs and box size, use assume
> isolated, decreasing and changing the mixing scheme and etc) and nothing
> works.
>
> The unique calculation that works fine for vacuum is the one with a box
> size of 7.9 x 7.9 x 7.9 A. I really don't understand why it only works for
> this specific box size.
>
> I ran several other charged systems (+1, +2 and -1 total charge) and all of
> them worked fine. The problem appears for -2 total charge in vacuum.
>
> Would some of you kindly help me in this?
>
> Cheers,
>
> Dr. Ernane de Freitas Martins
> Postdoctoral researcher
> IF - USP
> São Paulo, SP - Brazil

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<mailto:giuseppe.mattioli at ism.cnr.it>>

_______________________________________________
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https://lists.quantum-espresso.org/mailman/listinfo/users
_______________________________________________
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On Mar 15, 2019 7:30 PM, Michal Krompiec <michal.krompiec at gmail.com> wrote:
Dear Ernane,
Have you thought of using a more sophisticated method (like GW) on [CO3]- to calculate its EA? This would give you the energy of [CO3]2- in vacuum.
Best,
Michal Krompiec
University of Southampton & Merck KGaA

On Fri, 15 Mar 2019 at 18:22, Ernane de Freitas Martins <ernanefmg at gmail.com<mailto:ernanefmg at gmail.com>> wrote:
Dear Giuseppe,

I really appreciate your answer. Thank you very much for using your time to answer my question.

I'll think on your suggestion about trying hybrid functionals. The point is that I need to estimate the solvation energy for carbonate ion using the environ module, then I'll need to run a vacuum calculation using the same functional I'm already using rVV-10).

Thank you again for replying.

Atenciosamente,

Dr. Ernane de Freitas Martins
Postdoctoral researcher
IF - USP
São Paulo, SP - Brazil

Em sex, 15 de mar de 2019 15:04, Giuseppe Mattioli <giuseppe.mattioli at ism.cnr.it<mailto:giuseppe.mattioli at ism.cnr.it>> escreveu:

Dear Ernane
Your question contains part of the answer! Carbonate ion (CO3 2-) is
not stable outside water, and calculations of its properties in gas
phase are likely not so meaningful, but in the case of model
thermodynamics cycles (e.g. Born-Haber). The excess negative charge is
unbound when not stabilized by a strongly polar solvent, and this is
likely responsible for instabilities in the construction of the
Kohn-Sham potential along scf iterations. Moreover, this happens on
top of the strong delocalization error you experience when you use a
standard GGA exchange-correlation functional, when the
self-interaction of strongly localized electrons in the J[n] Coulomb
potential is not cancelled by a same term in the semi local exchange
potential. You may minimize this latter source of error by using a
hybrid GGA-EXX functional such as B3LYP, where the non local
Hartree-Fock part of the exchange functional can recover part of the
delocalization error, but you are not free yet from the instability of
carbonate in gas phase.
HTH
Giuseppe

Ernane de Freitas Martins <ernanefmg at gmail.com<mailto:ernanefmg at gmail.com>> ha scritto:

> Hello,
>
> I'm experiencing a problem to run a negatively charge molecule in quantum
> espresso. The system is CO32-.
>
> I try both vacuum and solvated (environ) calculations. The solvated one
> works fine.
>
> The problem is the calculation in vacuum. It never give the first ionic
> step because the SCF accuracy never reaches the convence criterion.
>
> I tried many different solutions (increase cutoffs and box size, use assume
> isolated, decreasing and changing the mixing scheme and etc) and nothing
> works.
>
> The unique calculation that works fine for vacuum is the one with a box
> size of 7.9 x 7.9 x 7.9 A. I really don't understand why it only works for
> this specific box size.
>
> I ran several other charged systems (+1, +2 and -1 total charge) and all of
> them worked fine. The problem appears for -2 total charge in vacuum.
>
> Would some of you kindly help me in this?
>
> Cheers,
>
> Dr. Ernane de Freitas Martins
> Postdoctoral researcher
> IF - USP
> São Paulo, SP - Brazil

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<mailto:giuseppe.mattioli at ism.cnr.it>>

_______________________________________________
users mailing list
users at lists.quantum-espresso.org<mailto:users at lists.quantum-espresso.org>
https://lists.quantum-espresso.org/mailman/listinfo/users
_______________________________________________
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https://lists.quantum-espresso.org/mailman/listinfo/users
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