<div dir="auto"><div dir="auto">Dear all,<div dir="auto"><br></div><div dir="auto">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. </div><div dir="auto"><br></div><div dir="auto">Is there a way of estimating this Jellium contribution and somehow discount it from the total energy?</div><div dir="auto"><br></div><div dir="auto">Is this necessary? </div><div dir="auto"><br></div><div dir="auto">The assume isolated schemes deal with this and already provide a correct energy?</div><div dir="auto"><br></div><div dir="auto">As I have mentioned, I didn't find further information about Jellium in QE documentation.</div><div dir="auto"><br></div><div dir="auto">Could some one clarify that to us or suggest a paper on this?</div><div dir="auto"><br><div data-smartmail="gmail_signature" dir="auto">Cheers,<br><br>Dr. Ernane de Freitas Martins<br>Postdoctoral researcher<br>IF - USP<br>São Paulo, SP - Brazil</div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Em seg, 18 de mar de 2019 06:28, Laurens Siemons <<a href="mailto:laurenssiemons@hotmail.be" target="_blank" rel="noreferrer">laurenssiemons@hotmail.be</a>> escreveu:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">
<div style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
Dear QE-users,</div>
<div style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<br>
</div>
<div style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
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?</div>
<div style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
<br>
</div>
<div style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
With kind regards,<br>
Laurens Siemons<br>
PhD, UAntwerp (Belgium)</div>
<div>
<hr style="display:inline-block;width:98%">
<div id="m_7230345978540160187m_8610746710222801013divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>Van:</b> users <<a href="mailto:users-bounces@lists.quantum-espresso.org" rel="noreferrer noreferrer" target="_blank">users-bounces@lists.quantum-espresso.org</a>> namens Nattino Francesco <<a href="mailto:francesco.nattino@epfl.ch" rel="noreferrer noreferrer" target="_blank">francesco.nattino@epfl.ch</a>><br>
<b>Verzonden:</b> zaterdag 16 maart 2019 9:02<br>
<b>Aan:</b> Quantum Espresso users Forum<br>
<b>Onderwerp:</b> Re: [QE-users] Negatively charged isolated molecule</font>
<div> </div>
</div>
<div>
<div dir="auto">
<div dir="auto">
<div dir="auto" style="font-family:sans-serif">Dear Ernane,</div>
<div dir="auto" style="font-family:sans-serif"> </div>
<div dir="auto" style="font-family:sans-serif"> 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.</div>
<div dir="auto" style="font-family:sans-serif"><br>
</div>
<div dir="auto" style="font-family:sans-serif">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).</div>
<div dir="auto" style="font-family:sans-serif"><br>
</div>
<div dir="auto" style="font-family:sans-serif">Best regards,</div>
<div dir="auto" style="font-family:sans-serif"><br>
</div>
<div dir="auto" style="font-family:sans-serif">Francesco Nattino,</div>
<div dir="auto" style="font-family:sans-serif">EPFL</div>
</div>
<div><br>
<div class="m_7230345978540160187m_8610746710222801013x_elided-text">On Mar 15, 2019 7:30 PM, Michal Krompiec <<a href="mailto:michal.krompiec@gmail.com" rel="noreferrer noreferrer" target="_blank">michal.krompiec@gmail.com</a>> wrote:<br type="attribution">
<blockquote style="margin:0 0 0 0.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<div>
<div dir="auto">Dear Ernane,</div>
</div>
<div dir="auto">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. </div>
<div>
<div dir="auto">Best,</div>
<div dir="auto">Michal Krompiec </div>
<div dir="auto">University of Southampton & Merck KGaA</div>
<br>
<div class="m_7230345978540160187m_8610746710222801013x_elided-text">
<div dir="ltr">On Fri, 15 Mar 2019 at 18:22, Ernane de Freitas Martins <<a href="mailto:ernanefmg@gmail.com" rel="noreferrer noreferrer" target="_blank">ernanefmg@gmail.com</a>> wrote:<br>
</div>
<blockquote style="margin:0 0 0 0.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="auto">
<div>Dear Giuseppe, </div>
<div dir="auto"><br>
</div>
<div dir="auto">I really appreciate your answer. Thank you very much for using your time to answer my question.</div>
<div dir="auto"><br>
</div>
<div dir="auto">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).</div>
<div dir="auto"><br>
</div>
<div dir="auto">Thank you again for replying.<br>
<br>
<div dir="auto">Atenciosamente,</div>
</div>
</div>
<div dir="auto">
<div dir="auto">
<div dir="auto"><br>
<br>
Dr. Ernane de Freitas Martins<br>
Postdoctoral researcher<br>
IF - USP<br>
São Paulo, SP - Brazil</div>
<br>
<div dir="auto" class="m_7230345978540160187m_8610746710222801013x_elided-text">
<div dir="ltr">Em sex, 15 de mar de 2019 15:04, Giuseppe Mattioli <<a href="mailto:giuseppe.mattioli@ism.cnr.it" rel="noreferrer noreferrer" target="_blank">giuseppe.mattioli@ism.cnr.it</a>> escreveu:<br>
</div>
<blockquote style="margin:0 0 0 0.8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
Dear Ernane<br>
Your question contains part of the answer! Carbonate ion (CO3 2-) is <br>
not stable outside water, and calculations of its properties in gas <br>
phase are likely not so meaningful, but in the case of model <br>
thermodynamics cycles (e.g. Born-Haber). The excess negative charge is <br>
unbound when not stabilized by a strongly polar solvent, and this is <br>
likely responsible for instabilities in the construction of the <br>
Kohn-Sham potential along scf iterations. Moreover, this happens on <br>
top of the strong delocalization error you experience when you use a <br>
standard GGA exchange-correlation functional, when the <br>
self-interaction of strongly localized electrons in the J[n] Coulomb <br>
potential is not cancelled by a same term in the semi local exchange <br>
potential. You may minimize this latter source of error by using a <br>
hybrid GGA-EXX functional such as B3LYP, where the non local <br>
Hartree-Fock part of the exchange functional can recover part of the <br>
delocalization error, but you are not free yet from the instability of <br>
carbonate in gas phase.<br>
HTH<br>
Giuseppe<br>
<br>
Ernane de Freitas Martins <<a href="mailto:ernanefmg@gmail.com" rel="noreferrer noreferrer" target="_blank">ernanefmg@gmail.com</a>> ha scritto:<br>
<br>
> Hello,<br>
><br>
> I'm experiencing a problem to run a negatively charge molecule in quantum<br>
> espresso. The system is CO32-.<br>
><br>
> I try both vacuum and solvated (environ) calculations. The solvated one<br>
> works fine.<br>
><br>
> The problem is the calculation in vacuum. It never give the first ionic<br>
> step because the SCF accuracy never reaches the convence criterion.<br>
><br>
> I tried many different solutions (increase cutoffs and box size, use assume<br>
> isolated, decreasing and changing the mixing scheme and etc) and nothing<br>
> works.<br>
><br>
> The unique calculation that works fine for vacuum is the one with a box<br>
> size of 7.9 x 7.9 x 7.9 A. I really don't understand why it only works for<br>
> this specific box size.<br>
><br>
> I ran several other charged systems (+1, +2 and -1 total charge) and all of<br>
> them worked fine. The problem appears for -2 total charge in vacuum.<br>
><br>
> Would some of you kindly help me in this?<br>
><br>
> Cheers,<br>
><br>
> Dr. Ernane de Freitas Martins<br>
> Postdoctoral researcher<br>
> IF - USP<br>
> São Paulo, SP - Brazil<br>
<br>
<br>
<br>
GIUSEPPE MATTIOLI<br>
CNR - ISTITUTO DI STRUTTURA DELLA MATERIA<br>
Via Salaria Km 29,300 - C.P. 10<br>
I-00015 - Monterotondo Scalo (RM)<br>
Mob (*preferred*) +39 373 7305625<br>
Tel + 39 06 90672342 - Fax +39 06 90672316<br>
E-mail: <<a href="mailto:giuseppe.mattioli@ism.cnr.it" rel="noreferrer noreferrer" target="_blank">giuseppe.mattioli@ism.cnr.it</a>><br>
<br>
_______________________________________________<br>
users mailing list<br>
<a href="mailto:users@lists.quantum-espresso.org" rel="noreferrer noreferrer" target="_blank">users@lists.quantum-espresso.org</a><br>
<a href="https://lists.quantum-espresso.org/mailman/listinfo/users" rel="noreferrer noreferrer" target="_blank">https://lists.quantum-espresso.org/mailman/listinfo/users</a></blockquote>
</div>
</div>
</div>
_______________________________________________<br>
users mailing list<br>
<a href="mailto:users@lists.quantum-espresso.org" rel="noreferrer noreferrer" target="_blank">users@lists.quantum-espresso.org</a><br>
<a href="https://lists.quantum-espresso.org/mailman/listinfo/users" rel="noreferrer noreferrer" target="_blank">https://lists.quantum-espresso.org/mailman/listinfo/users</a></blockquote>
</div>
</div>
</div>
</blockquote>
</div>
<br>
</div>
</div>
<div class="m_7230345978540160187m_8610746710222801013x_gmail_extra"><br>
<div class="m_7230345978540160187m_8610746710222801013x_gmail_quote">On Mar 15, 2019 7:30 PM, Michal Krompiec <<a href="mailto:michal.krompiec@gmail.com" rel="noreferrer noreferrer" target="_blank">michal.krompiec@gmail.com</a>> wrote:<br type="attribution">
</div>
</div>
<div>
<div>
<div dir="auto">Dear Ernane,</div>
</div>
<div dir="auto">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. </div>
<div>
<div dir="auto">Best,</div>
<div dir="auto">Michal Krompiec </div>
<div dir="auto">University of Southampton & Merck KGaA</div>
<br>
<div class="m_7230345978540160187m_8610746710222801013x_gmail_quote">
<div dir="ltr" class="m_7230345978540160187m_8610746710222801013x_gmail_attr">On Fri, 15 Mar 2019 at 18:22, Ernane de Freitas Martins <<a href="mailto:ernanefmg@gmail.com" rel="noreferrer noreferrer" target="_blank">ernanefmg@gmail.com</a>> wrote:<br>
</div>
<blockquote class="m_7230345978540160187m_8610746710222801013x_gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="auto">
<div>Dear Giuseppe, </div>
<div dir="auto"><br>
</div>
<div dir="auto">I really appreciate your answer. Thank you very much for using your time to answer my question.</div>
<div dir="auto"><br>
</div>
<div dir="auto">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).</div>
<div dir="auto"><br>
</div>
<div dir="auto">Thank you again for replying.<br>
<br>
<div dir="auto">Atenciosamente,</div>
</div>
</div>
<div dir="auto">
<div dir="auto">
<div dir="auto"><br>
<br>
Dr. Ernane de Freitas Martins<br>
Postdoctoral researcher<br>
IF - USP<br>
São Paulo, SP - Brazil</div>
<br>
<div class="m_7230345978540160187m_8610746710222801013x_gmail_quote" dir="auto">
<div dir="ltr" class="m_7230345978540160187m_8610746710222801013x_gmail_attr">Em sex, 15 de mar de 2019 15:04, Giuseppe Mattioli <<a href="mailto:giuseppe.mattioli@ism.cnr.it" rel="noreferrer noreferrer" target="_blank">giuseppe.mattioli@ism.cnr.it</a>> escreveu:<br>
</div>
<blockquote class="m_7230345978540160187m_8610746710222801013x_gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
Dear Ernane<br>
Your question contains part of the answer! Carbonate ion (CO3 2-) is <br>
not stable outside water, and calculations of its properties in gas <br>
phase are likely not so meaningful, but in the case of model <br>
thermodynamics cycles (e.g. Born-Haber). The excess negative charge is <br>
unbound when not stabilized by a strongly polar solvent, and this is <br>
likely responsible for instabilities in the construction of the <br>
Kohn-Sham potential along scf iterations. Moreover, this happens on <br>
top of the strong delocalization error you experience when you use a <br>
standard GGA exchange-correlation functional, when the <br>
self-interaction of strongly localized electrons in the J[n] Coulomb <br>
potential is not cancelled by a same term in the semi local exchange <br>
potential. You may minimize this latter source of error by using a <br>
hybrid GGA-EXX functional such as B3LYP, where the non local <br>
Hartree-Fock part of the exchange functional can recover part of the <br>
delocalization error, but you are not free yet from the instability of <br>
carbonate in gas phase.<br>
HTH<br>
Giuseppe<br>
<br>
Ernane de Freitas Martins <<a href="mailto:ernanefmg@gmail.com" rel="noreferrer noreferrer noreferrer" target="_blank">ernanefmg@gmail.com</a>> ha scritto:<br>
<br>
> Hello,<br>
><br>
> I'm experiencing a problem to run a negatively charge molecule in quantum<br>
> espresso. The system is CO32-.<br>
><br>
> I try both vacuum and solvated (environ) calculations. The solvated one<br>
> works fine.<br>
><br>
> The problem is the calculation in vacuum. It never give the first ionic<br>
> step because the SCF accuracy never reaches the convence criterion.<br>
><br>
> I tried many different solutions (increase cutoffs and box size, use assume<br>
> isolated, decreasing and changing the mixing scheme and etc) and nothing<br>
> works.<br>
><br>
> The unique calculation that works fine for vacuum is the one with a box<br>
> size of 7.9 x 7.9 x 7.9 A. I really don't understand why it only works for<br>
> this specific box size.<br>
><br>
> I ran several other charged systems (+1, +2 and -1 total charge) and all of<br>
> them worked fine. The problem appears for -2 total charge in vacuum.<br>
><br>
> Would some of you kindly help me in this?<br>
><br>
> Cheers,<br>
><br>
> Dr. Ernane de Freitas Martins<br>
> Postdoctoral researcher<br>
> IF - USP<br>
> São Paulo, SP - Brazil<br>
<br>
<br>
<br>
GIUSEPPE MATTIOLI<br>
CNR - ISTITUTO DI STRUTTURA DELLA MATERIA<br>
Via Salaria Km 29,300 - C.P. 10<br>
I-00015 - Monterotondo Scalo (RM)<br>
Mob (*preferred*) +39 373 7305625<br>
Tel + 39 06 90672342 - Fax +39 06 90672316<br>
E-mail: <<a href="mailto:giuseppe.mattioli@ism.cnr.it" rel="noreferrer noreferrer noreferrer" target="_blank">giuseppe.mattioli@ism.cnr.it</a>><br>
<br>
_______________________________________________<br>
users mailing list<br>
<a href="mailto:users@lists.quantum-espresso.org" rel="noreferrer noreferrer noreferrer" target="_blank">users@lists.quantum-espresso.org</a><br>
<a href="https://lists.quantum-espresso.org/mailman/listinfo/users" rel="noreferrer noreferrer noreferrer noreferrer" target="_blank">https://lists.quantum-espresso.org/mailman/listinfo/users</a></blockquote>
</div>
</div>
</div>
_______________________________________________<br>
users mailing list<br>
<a href="mailto:users@lists.quantum-espresso.org" rel="noreferrer noreferrer" target="_blank">users@lists.quantum-espresso.org</a><br>
<a href="https://lists.quantum-espresso.org/mailman/listinfo/users" rel="noreferrer noreferrer noreferrer" target="_blank">https://lists.quantum-espresso.org/mailman/listinfo/users</a></blockquote>
</div>
</div>
</div>
</div>
</div>
</div>
_______________________________________________<br>
users mailing list<br>
<a href="mailto:users@lists.quantum-espresso.org" rel="noreferrer noreferrer" target="_blank">users@lists.quantum-espresso.org</a><br>
<a href="https://lists.quantum-espresso.org/mailman/listinfo/users" rel="noreferrer noreferrer noreferrer" target="_blank">https://lists.quantum-espresso.org/mailman/listinfo/users</a></blockquote></div></div>