[QE-users] Negatively charged isolated molecule

Mon Mar 18 10:49:02 CET 2019

Dear all,

regarding energy calculations of charged systems in general, I also have
doubts about the Jellium contribution to the total energy. The unique
mention to Jellium I found is the phrase in the input description saying
that a background Jellium is added for charged calculations. Thus I have
some doubts.

Is there a way of estimating this Jellium contribution and somehow discount
it from the total energy?

Is this necessary?

The assume isolated schemes deal with this and already provide a correct
energy?

As I have mentioned, I didn't find further information about Jellium in QE
documentation.

Could some one clarify that to us or suggest a paper on this?

Cheers,

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

Em seg, 18 de mar de 2019 06:28, Laurens Siemons <laurenssiemons at hotmail.be>
escreveu:

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