<div dir="ltr"><div dir="ltr"><div dir="ltr">Actually there was a bug: when using tetrahedra, the code did not write the Fermi energy to data file. It is fixed by this patch: <a href="https://gitlab.com/QEF/q-e/merge_requests/378">https://gitlab.com/QEF/q-e/merge_requests/378</a>. Thank you for reporting this problem</div><div dir="ltr"><br></div><div>Paolo<br></div><div dir="ltr"><br></div><div dir="ltr"><a href="https://gitlab.com/QEF/q-e/merge_requests/378">https://gitlab.com/QEF/q-e/merge_requests/378</a><br></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sun, Mar 17, 2019 at 11:27 AM Sylwia Golab <<a href="mailto:Sylwia.Golab@fis.agh.edu.pl">Sylwia.Golab@fis.agh.edu.pl</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div style="font-family:Tahoma,sans-serif;font-size:13px"><div>Dear Mr Giannozzi,</div><div><br></div>Thank you for you reply and sincerely apologize for the wrong guess I have made.<div>The problem appears with qe-6.4 compiled with intel v. 11 as well as with the one comming from Parallel Studio 2017. It does not appear with qe-6.3 compiled on the same machines. My example input files (problem appears also with other, more realistic inputs) are as follows:</div><div><b><a href="http://scf.in" target="_blank">scf.in</a>:</b></div><div> &control<br> calculation='scf'<br> restart_mode='from_scratch',<br> prefix='Nb',<br> pseudo_dir = '/home/student3/qe/qe-6.0/pseudo/',<br> outdir='./tmp_dir/'<br> /<br> &system<br> ibrav= 3, celldm(1)=6.250946058252, nat= 1, ntyp= 1,<br> ecutwfc =50, ecutrho=600,<br> occupations="smearing", smearing="m-v", degauss=0.02<br> /<br> &electrons<br> conv_thr = 1.0e-11<br> mixing_beta = 0.7<br> /<br>ATOMIC_SPECIES<br> Nb 92.906 Nb.pbe-spn-rrkjus_psl.1.0.0.UPF<br>ATOMIC_POSITIONS<br> Nb 0.00 0.00 0.00<br>K_POINTS automatic<br>4 4 4 0 0 0<br></div><div><br></div><div><b><a href="http://dos.in" target="_blank">dos.in</a></b></div><div> &control<br> calculation='nscf'<br> restart_mode='from_scratch',<br> prefix='Nb',<br> pseudo_dir = '/home/student3/qe/qe-6.0/pseudo/',<br> outdir='./tmp_dir/'<br> /<br> &system<br> ibrav= 3, celldm(1)=6.250946058252, nat= 1, ntyp= 1,<br> ecutwfc =50, ecutrho=600,<br> occupations="tetrahedra" <br> /<br> &electrons<br> conv_thr = 1.0e-11<br> mixing_beta = 0.7<br> /<br>ATOMIC_SPECIES<br> Nb 92.906 Nb.pbe-spn-rrkjus_psl.1.0.0.UPF<br>ATOMIC_POSITIONS<br> Nb 0.00 0.00 0.00<br>K_POINTS automatic<br>4 4 4 0 0 0<br></div><div><br></div><div><b><a href="http://fs.in" target="_blank">fs.in</a></b></div><div>&fermi<br> outdir='./tmp_dir/'<br> prefix='Nb'<br>/<br></div><div><br></div><div>Firstly I am running <i>mpirun -np 4 pw.x <<a href="http://scf.in" target="_blank">scf.in</a> >scf.out </i>and I can grep Fermi energy from *xml files: <br></div><div><i>[student3 qe4]$ grep fermi tmp_dir/*<br>tmp_dir/Nb.xml: <fermi_energy>6.529259765371975e-1</fermi_energy</i>></div><div><br></div><div>Then I am running <i>mpirun -np 4 pw.x<<a href="http://dos.in" target="_blank">dos.in</a> >dos.out </i>and now I cannot see the Fermi energy in *xml<i>:</i></div><div><i>[student3 qe4]$ grep fermi tmp_dir/* (nothing appears)</i></div><div><i><br></i></div><div>But for sure the Fermi energy is computed in nscf cycle, because I can grep it from dos.out file:</div><div>[student3 qe4]$ grep Fermi *<br>dos.out: the Fermi energy is 18.0671 ev<br>scf.out: the Fermi energy is 17.7670 ev<br></div><div><br></div><div>As I mentioned before, after running <i>mpirun -np 4 fs.x<<a href="http://fs.in" target="_blank">fs.in</a> >fs.out</i> I see in the fs.out file the line:<br></div><div><i> 1 bands found crossing Ef = 0.000000</i><br><br></div><div>When I changed the fermisurface.f90 such that it is reading Fermi energy from dos.out, then the program fs.x works very well (in agreement with the results obtained with qe-6.3).<br></div><div><br></div><div>I would like to thank you for your help in advance.</div><div>Best regards,</div><div>Sylwia</div><div><br></div><div><br></div><div>>>> <<a href="mailto:users-request@lists.quantum-espresso.org" target="_blank">users-request@lists.quantum-espresso.org</a>> 03/16/19 12:02 PM >>><br></div>Send users mailing list submissions to<br> <a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a><br><br>To subscribe or unsubscribe via the World Wide Web, visit<br> <a href="https://lists.quantum-espresso.org/mailman/listinfo/users" target="_blank">https://lists.quantum-espresso.org/mailman/listinfo/users</a><br>or, via email, send a message with subject or body 'help' to<br> <a href="mailto:users-request@lists.quantum-espresso.org" target="_blank">users-request@lists.quantum-espresso.org</a><br><br>You can reach the person managing the list at<br> <a href="mailto:users-owner@lists.quantum-espresso.org" target="_blank">users-owner@lists.quantum-espresso.org</a><br><br>When replying, please edit your Subject line so it is more specific<br>than "Re: Contents of users digest..."<br><br><br>Today's Topics:<br><br> 1. Negatively charged isolated molecule (Ernane de Freitas Martins)<br> 2. qe-6.4: problem with fs.x (Sylwia Golab)<br> 3. Re: Negatively charged isolated molecule (Giuseppe Mattioli)<br> 4. Re: Negatively charged isolated molecule<br> (Ernane de Freitas Martins)<br> 5. Re: Negatively charged isolated molecule (Michal Krompiec)<br> 6. Re: How to calculate water molecule energy at large cell<br> size? (Paolo Giannozzi)<br> 7. Re: qe-6.4: problem with fs.x (Paolo Giannozzi)<br> 8. Re: Negatively charged isolated molecule (Nattino Francesco)<br> 9. How can read constant velocity from input file when<br> restart_mode= 'restart' (=?ISO-8859-1?B?THUgSGFpbGluIA==?=)<br><br><br>----------------------------------------------------------------------<br><br>Message: 1<br>Date: Fri, 15 Mar 2019 13:54:49 -0300<br>From: Ernane de Freitas Martins <<a href="mailto:ernanefmg@gmail.com" target="_blank">ernanefmg@gmail.com</a>><br>To: <a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a><br>Subject: [QE-users] Negatively charged isolated molecule<br>Message-ID:<br> <<a href="mailto:CAFMPbVWG4VAvpsHjyGULPdbyhafpL7X15xfKAbVGuZgMEoDimA@mail.gmail.com" target="_blank">CAFMPbVWG4VAvpsHjyGULPdbyhafpL7X15xfKAbVGuZgMEoDimA@mail.gmail.com</a>><br>Content-Type: text/plain; charset="utf-8"<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>S?o Paulo, SP - Brazil<br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <<a href="http://lists.quantum-espresso.org/pipermail/users/attachments/20190315/17f0bf2c/attachment-0001.html" target="_blank">http://lists.quantum-espresso.org/pipermail/users/attachments/20190315/17f0bf2c/attachment-0001.html</a>><br><br>------------------------------<br><br>Message: 2<br>Date: Fri, 15 Mar 2019 18:56:38 +0100<br>From: "Sylwia Golab" <<a href="mailto:Sylwia.Golab@fis.agh.edu.pl" target="_blank">Sylwia.Golab@fis.agh.edu.pl</a>><br>To: <<a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a>><br>Subject: [QE-users] qe-6.4: problem with fs.x<br>Message-ID: <<a href="mailto:5C8BF566020000D400029CFA@orion.fis.agh.edu.pl" target="_blank">5C8BF566020000D400029CFA@orion.fis.agh.edu.pl</a>><br>Content-Type: text/plain; charset="us-ascii"<br><br>Dear all,<br><br><br>the program fs.x in the qe-6.4 package gives me a messages:<br> Message from routine pw_readschema_file:<br> failed retrieving input info from xml file, please check it<br>and:<br><br> 1 bands found crossing Ef = 0.000000<br><br>so it cannot read Fermi energy.<br><br><br><br>As far as I understand, the problem is, that in the 6.4 version of qe the line<br><br>...<br>has been removed from tmp_dir/case.xml as well as from tmp_dir/case.save/data-file-schema.xml files.<br>Also I cannot find any other information about Fermi energy in these *.xml files.<br><br><br>Does anyone know how to workaround this problem?<br><br><br><br>Regards,Sylwia<br><br><br><br><br><br><br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <<a href="http://lists.quantum-espresso.org/pipermail/users/attachments/20190315/881191ee/attachment-0001.html" target="_blank">http://lists.quantum-espresso.org/pipermail/users/attachments/20190315/881191ee/attachment-0001.html</a>><br><br>------------------------------<br><br>Message: 3<br>Date: Fri, 15 Mar 2019 19:04:15 +0100<br>From: Giuseppe Mattioli <<a href="mailto:giuseppe.mattioli@ism.cnr.it" target="_blank">giuseppe.mattioli@ism.cnr.it</a>><br>To: <a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a><br>Subject: Re: [QE-users] Negatively charged isolated molecule<br>Message-ID:<br> <<a href="mailto:20190315190415.Horde.meqRST7PDvkj-9gJDJxiN7w@webmail.sic.rm.cnr.it" target="_blank">20190315190415.Horde.meqRST7PDvkj-9gJDJxiN7w@webmail.sic.rm.cnr.it</a>><br>Content-Type: text/plain; charset=utf-8; format=flowed; DelSp=Yes<br><br><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" 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>> S?o 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" target="_blank">giuseppe.mattioli@ism.cnr.it</a>><br><br><br><br>------------------------------<br><br>Message: 4<br>Date: Fri, 15 Mar 2019 15:21:39 -0300<br>From: Ernane de Freitas Martins <<a href="mailto:ernanefmg@gmail.com" target="_blank">ernanefmg@gmail.com</a>><br>To: Quantum Espresso users Forum <<a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a>><br>Subject: Re: [QE-users] Negatively charged isolated molecule<br>Message-ID:<br> <CAFMPbVW75y_YnX=e=<a href="mailto:JrjB6Dhs8E6bpbxk5b6twxgcRpehYme4Q@mail.gmail.com" target="_blank">JrjB6Dhs8E6bpbxk5b6twxgcRpehYme4Q@mail.gmail.com</a>><br>Content-Type: text/plain; charset="utf-8"<br><br>Dear Giuseppe,<br><br>I really appreciate your answer. Thank you very much for using your time to<br>answer my question.<br><br>I'll think on your suggestion about trying hybrid functionals. The point is<br>that I need to estimate the solvation energy for carbonate ion using the<br>environ module, then I'll need to run a vacuum calculation using the same<br>functional I'm already using rVV-10).<br><br>Thank you again for replying.<br><br>Atenciosamente,<br><br>Dr. Ernane de Freitas Martins<br>Postdoctoral researcher<br>IF - USP<br>S?o Paulo, SP - Brazil<br><br>Em sex, 15 de mar de 2019 15:04, Giuseppe Mattioli <<br><a href="mailto:giuseppe.mattioli@ism.cnr.it" target="_blank">giuseppe.mattioli@ism.cnr.it</a>> escreveu:<br><br>><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" 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<br>> 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<br>> for<br>> > this specific box size.<br>> ><br>> > I ran several other charged systems (+1, +2 and -1 total charge) and all<br>> 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>> > S?o 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" target="_blank">giuseppe.mattioli@ism.cnr.it</a>><br>><br>> _______________________________________________<br>> users mailing list<br>> <a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a><br>> <a href="https://lists.quantum-espresso.org/mailman/listinfo/users" target="_blank">https://lists.quantum-espresso.org/mailman/listinfo/users</a><br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <<a href="http://lists.quantum-espresso.org/pipermail/users/attachments/20190315/586c49b9/attachment-0001.html" target="_blank">http://lists.quantum-espresso.org/pipermail/users/attachments/20190315/586c49b9/attachment-0001.html</a>><br><br>------------------------------<br><br>Message: 5<br>Date: Fri, 15 Mar 2019 18:29:16 +0000<br>From: Michal Krompiec <<a href="mailto:michal.krompiec@gmail.com" target="_blank">michal.krompiec@gmail.com</a>><br>To: Quantum Espresso users Forum <<a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a>><br>Subject: Re: [QE-users] Negatively charged isolated molecule<br>Message-ID:<br> <<a href="mailto:CAOWoSSP4oMKAmMyJzpoEVtQ3pa2j405MPFNKgSGOQbMVeOTr0A@mail.gmail.com" target="_blank">CAOWoSSP4oMKAmMyJzpoEVtQ3pa2j405MPFNKgSGOQbMVeOTr0A@mail.gmail.com</a>><br>Content-Type: text/plain; charset="utf-8"<br><br>Dear Ernane,<br>Have you thought of using a more sophisticated method (like GW) on [CO3]-<br>to calculate its EA? This would give you the energy of [CO3]2- in vacuum.<br>Best,<br>Michal Krompiec<br>University of Southampton & Merck KGaA<br><br>On Fri, 15 Mar 2019 at 18:22, Ernane de Freitas Martins <<a href="mailto:ernanefmg@gmail.com" target="_blank">ernanefmg@gmail.com</a>><br>wrote:<br><br>> Dear Giuseppe,<br>><br>> I really appreciate your answer. Thank you very much for using your time<br>> to answer my question.<br>><br>> I'll think on your suggestion about trying hybrid functionals. The point<br>> is that I need to estimate the solvation energy for carbonate ion using the<br>> environ module, then I'll need to run a vacuum calculation using the same<br>> functional I'm already using rVV-10).<br>><br>> Thank you again for replying.<br>><br>> Atenciosamente,<br>><br>><br>> Dr. Ernane de Freitas Martins<br>> Postdoctoral researcher<br>> IF - USP<br>> S?o Paulo, SP - Brazil<br>><br>> Em sex, 15 de mar de 2019 15:04, Giuseppe Mattioli <<br>> <a href="mailto:giuseppe.mattioli@ism.cnr.it" target="_blank">giuseppe.mattioli@ism.cnr.it</a>> escreveu:<br>><br>>><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" 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<br>>> 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<br>>> 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<br>>> for<br>>> > this specific box size.<br>>> ><br>>> > I ran several other charged systems (+1, +2 and -1 total charge) and<br>>> 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>>> > S?o 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" target="_blank">giuseppe.mattioli@ism.cnr.it</a>><br>>><br>>> _______________________________________________<br>>> users mailing list<br>>> <a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a><br>>> <a href="https://lists.quantum-espresso.org/mailman/listinfo/users" target="_blank">https://lists.quantum-espresso.org/mailman/listinfo/users</a><br>><br>> _______________________________________________<br>> users mailing list<br>> <a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a><br>> <a href="https://lists.quantum-espresso.org/mailman/listinfo/users" target="_blank">https://lists.quantum-espresso.org/mailman/listinfo/users</a><br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <<a href="http://lists.quantum-espresso.org/pipermail/users/attachments/20190315/0b06d502/attachment-0001.html" target="_blank">http://lists.quantum-espresso.org/pipermail/users/attachments/20190315/0b06d502/attachment-0001.html</a>><br><br>------------------------------<br><br>Message: 6<br>Date: Fri, 15 Mar 2019 22:37:45 +0100<br>From: Paolo Giannozzi <<a href="mailto:p.giannozzi@gmail.com" target="_blank">p.giannozzi@gmail.com</a>><br>To: Quantum Espresso users Forum <<a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a>><br>Subject: Re: [QE-users] How to calculate water molecule energy at<br> large cell size?<br>Message-ID:<br> <CAPMgbCs+Q7+2f_FqtmvdBSfSaHm_Ymt4fKay9ZXAVA6FVOQt=<a href="mailto:g@mail.gmail.com" target="_blank">g@mail.gmail.com</a>><br>Content-Type: text/plain; charset="utf-8"<br><br>SCAN is numerically better behaved than other Meta-GGA's, but cells with a<br>lot of empty space are still problematic. See for instance this:<br><a href="https://gitlab.com/QEF/q-e/issues/32" target="_blank">https://gitlab.com/QEF/q-e/issues/32</a><br><br>Paolo<br><br>On Fri, Mar 15, 2019 at 1:55 AM ? ?? <<a href="mailto:alingjing@outlook.com" target="_blank">alingjing@outlook.com</a>> wrote:<br><br>> Hello,<br>><br>><br>><br>> My question is how to calculate scf energy of water molecule in large cell<br>> size of 12 angstrom. The energy cutoff is at 160 ry. The dft method I used<br>> is scan. Mixing_beta=0.1 and diagonalization = 'cg?. When the cell size is<br>> beyond 16 bohr the program reported ?too many bands are not converged and<br>> estimated scf accuracy is too large.<br>><br>><br>><br>> I?m wondering if there is any other options I can add in my input to make<br>> scf energy converged for water molecule in large box?<br>><br>><br>><br>> Thanks,<br>><br>> Jing<br>><br>> University of delaware<br>><br>> _______________________________________________<br>> users mailing list<br>> <a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a><br>> <a href="https://lists.quantum-espresso.org/mailman/listinfo/users" target="_blank">https://lists.quantum-espresso.org/mailman/listinfo/users</a><br><br><br><br>-- <br>Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,<br>Univ. Udine, via delle Scienze 208, 33100 Udine, Italy<br>Phone +39-0432-558216, fax +39-0432-558222<br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <<a href="http://lists.quantum-espresso.org/pipermail/users/attachments/20190315/21650365/attachment-0001.html" target="_blank">http://lists.quantum-espresso.org/pipermail/users/attachments/20190315/21650365/attachment-0001.html</a>><br><br>------------------------------<br><br>Message: 7<br>Date: Fri, 15 Mar 2019 22:46:22 +0100<br>From: Paolo Giannozzi <<a href="mailto:p.giannozzi@gmail.com" target="_blank">p.giannozzi@gmail.com</a>><br>To: Quantum Espresso users Forum <<a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a>><br>Subject: Re: [QE-users] qe-6.4: problem with fs.x<br>Message-ID:<br> <<a href="mailto:CAPMgbCtQSnF9eGXJbhFPMyQ4o8nRpemiHXPWhG2sbv7Wz9q47Q@mail.gmail.com" target="_blank">CAPMgbCtQSnF9eGXJbhFPMyQ4o8nRpemiHXPWhG2sbv7Wz9q47Q@mail.gmail.com</a>><br>Content-Type: text/plain; charset="utf-8"<br><br>On Fri, Mar 15, 2019 at 6:57 PM Sylwia Golab <<a href="mailto:Sylwia.Golab@fis.agh.edu.pl" target="_blank">Sylwia.Golab@fis.agh.edu.pl</a>><br>wrote:<br><br>><br>> the program fs.x in the qe-6.4 package gives me a messages:<br>><br>> * Message from routine pw_readschema_file: failed retrieving input<br>> info from xml file, please check it*<br>><br><br>are you using Intel v.12? it should not be a problem, the input is not<br>currently read from xml<br><br>As far as I understand, the problem is, that in the 6.4 version of qe the<br>> line<br>> *<fermi_energy>...</fermi_energy>*<br>> has been removed from tmp_dir/case.xml<br>><br><br>I don't think so<br><br>Also I cannot find any other information about Fermi energy in these *.xml<br>> files.<br>><br><br>if the Fermi energy is not in the xml files, it hasn't been computed.<br><br>><br>> Does anyone know how to workaround this problem?<br>><br><br>unlikely, without knowing exactly what you did<br><br>Paolo<br><br><br><br>> Regards,<br>> Sylwia<br>><br>><br>> _______________________________________________<br>> users mailing list<br>> <a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a><br>> <a href="https://lists.quantum-espresso.org/mailman/listinfo/users" target="_blank">https://lists.quantum-espresso.org/mailman/listinfo/users</a><br><br><br><br>-- <br>Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,<br>Univ. Udine, via delle Scienze 208, 33100 Udine, Italy<br>Phone +39-0432-558216, fax +39-0432-558222<br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <<a href="http://lists.quantum-espresso.org/pipermail/users/attachments/20190315/b12e88b4/attachment-0001.html" target="_blank">http://lists.quantum-espresso.org/pipermail/users/attachments/20190315/b12e88b4/attachment-0001.html</a>><br><br>------------------------------<br><br>Message: 8<br>Date: Sat, 16 Mar 2019 08:02:05 +0000<br>From: Nattino Francesco <<a href="mailto:francesco.nattino@epfl.ch" target="_blank">francesco.nattino@epfl.ch</a>><br>To: Quantum Espresso users Forum <<a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a>><br>Subject: Re: [QE-users] Negatively charged isolated molecule<br>Message-ID: <<a href="mailto:5459c922-ff5d-4de0-a4cc-32e935d1efd3@email.android.com" target="_blank">5459c922-ff5d-4de0-a4cc-32e935d1efd3@email.android.com</a>><br>Content-Type: text/plain; charset="iso-8859-1"<br><br>Dear Ernane,<br><br> 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.<br><br>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).<br><br>Best regards,<br><br>Francesco Nattino,<br>EPFL<br><br>On Mar 15, 2019 7:30 PM, Michal Krompiec <<a href="mailto:michal.krompiec@gmail.com" target="_blank">michal.krompiec@gmail.com</a>> wrote:<br>Dear Ernane,<br>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.<br>Best,<br>Michal Krompiec<br>University of Southampton & Merck KGaA<br><br>On Fri, 15 Mar 2019 at 18:22, Ernane de Freitas Martins <<a href="mailto:ernanefmg@gmail.com" target="_blank">ernanefmg@gmail.com</a><mailto:<a href="mailto:ernanefmg@gmail.com" target="_blank">ernanefmg@gmail.com</a>>> wrote:<br>Dear Giuseppe,<br><br>I really appreciate your answer. Thank you very much for using your time to answer my question.<br><br>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).<br><br>Thank you again for replying.<br><br>Atenciosamente,<br><br><br>Dr. Ernane de Freitas Martins<br>Postdoctoral researcher<br>IF - USP<br>S?o Paulo, SP - Brazil<br><br>Em sex, 15 de mar de 2019 15:04, Giuseppe Mattioli <<a href="mailto:giuseppe.mattioli@ism.cnr.it" target="_blank">giuseppe.mattioli@ism.cnr.it</a><mailto:<a href="mailto:giuseppe.mattioli@ism.cnr.it" target="_blank">giuseppe.mattioli@ism.cnr.it</a>>> escreveu:<br><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" target="_blank">ernanefmg@gmail.com</a><mailto:<a href="mailto:ernanefmg@gmail.com" 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>> S?o 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" target="_blank">giuseppe.mattioli@ism.cnr.it</a><mailto:<a href="mailto:giuseppe.mattioli@ism.cnr.it" target="_blank">giuseppe.mattioli@ism.cnr.it</a>>><br><br>_______________________________________________<br>users mailing list<br><a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a><mailto:<a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a>><br><a href="https://lists.quantum-espresso.org/mailman/listinfo/users" target="_blank">https://lists.quantum-espresso.org/mailman/listinfo/users</a><br>_______________________________________________<br>users mailing list<br><a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a><mailto:<a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a>><br><a href="https://lists.quantum-espresso.org/mailman/listinfo/users" target="_blank">https://lists.quantum-espresso.org/mailman/listinfo/users</a><br><br><br>On Mar 15, 2019 7:30 PM, Michal Krompiec <<a href="mailto:michal.krompiec@gmail.com" target="_blank">michal.krompiec@gmail.com</a>> wrote:<br>Dear Ernane,<br>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.<br>Best,<br>Michal Krompiec<br>University of Southampton & Merck KGaA<br><br>On Fri, 15 Mar 2019 at 18:22, Ernane de Freitas Martins <<a href="mailto:ernanefmg@gmail.com" target="_blank">ernanefmg@gmail.com</a><mailto:<a href="mailto:ernanefmg@gmail.com" target="_blank">ernanefmg@gmail.com</a>>> wrote:<br>Dear Giuseppe,<br><br>I really appreciate your answer. Thank you very much for using your time to answer my question.<br><br>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).<br><br>Thank you again for replying.<br><br>Atenciosamente,<br><br><br>Dr. Ernane de Freitas Martins<br>Postdoctoral researcher<br>IF - USP<br>S?o Paulo, SP - Brazil<br><br>Em sex, 15 de mar de 2019 15:04, Giuseppe Mattioli <<a href="mailto:giuseppe.mattioli@ism.cnr.it" target="_blank">giuseppe.mattioli@ism.cnr.it</a><mailto:<a href="mailto:giuseppe.mattioli@ism.cnr.it" target="_blank">giuseppe.mattioli@ism.cnr.it</a>>> escreveu:<br><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" target="_blank">ernanefmg@gmail.com</a><mailto:<a href="mailto:ernanefmg@gmail.com" 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>> S?o 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" target="_blank">giuseppe.mattioli@ism.cnr.it</a><mailto:<a href="mailto:giuseppe.mattioli@ism.cnr.it" target="_blank">giuseppe.mattioli@ism.cnr.it</a>>><br><br>_______________________________________________<br>users mailing list<br><a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a><mailto:<a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a>><br><a href="https://lists.quantum-espresso.org/mailman/listinfo/users" target="_blank">https://lists.quantum-espresso.org/mailman/listinfo/users</a><br>_______________________________________________<br>users mailing list<br><a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a><mailto:<a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a>><br><a href="https://lists.quantum-espresso.org/mailman/listinfo/users" target="_blank">https://lists.quantum-espresso.org/mailman/listinfo/users</a><br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <<a href="http://lists.quantum-espresso.org/pipermail/users/attachments/20190316/c5a3cd79/attachment-0001.html" target="_blank">http://lists.quantum-espresso.org/pipermail/users/attachments/20190316/c5a3cd79/attachment-0001.html</a>><br><br>------------------------------<br><br>Message: 9<br>Date: Sat, 16 Mar 2019 17:29:07 +0800<br>From: "=?ISO-8859-1?B?THUgSGFpbGluIA==?=" <<a href="mailto:415005271@qq.com" target="_blank">415005271@qq.com</a>><br>To: "=?ISO-8859-1?B?dXNlcnM=?=" <<a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a>><br>Subject: [QE-users] How can read constant velocity from input file<br> when restart_mode= 'restart'<br>Message-ID: <<a href="mailto:tencent_73D1D71A3787D2E58285BFC014DBEE84C206@qq.com" target="_blank">tencent_73D1D71A3787D2E58285BFC014DBEE84C206@qq.com</a>><br>Content-Type: text/plain; charset="iso-8859-1"<br><br>Dear Paolo Giannozzi ,<br><br><br> I want to apply a constant velocity along the y direction on the upper atoms through the whole progress using cp.x in Quantum Espresso 6.1. version. <br><br><br><br>The Card: ATOMIC_VELOCITIES { a.u },in the the manual ,which shows that ion_velocities= 'from_input' : restart the simulation with atomic velocities read from standard input . <br><br>BEWARE: works only if restart_mode='from_scratch', tested only with electrons_dynamics='cg'.<br><br><br>The question is that if I read the input file with the card restart_mode='from_scratch',the constant velocity in the input file can be applyed ,while the information about electrons and ions after having been minimized and displaced from their equilibrium positions may be ignored. if I read the input file with the card restart_mode='restart',the constant velocity in the input file cannot be applyed.<br><br><br>If I have ignored something during the progress ?<br><br><br><br>Any help would be appreciated.<br><br><br><br>Thank you!<br>Best regards,<br><br><br><br>------<br><br>LU Hailin, Graduate Student<br><br>State Key Laboratory of Mechanical Transmission, Chongqing University<br><br>Chongqing 400044, China<br><br>Tel: (+86) 18362360286<br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <<a href="http://lists.quantum-espresso.org/pipermail/users/attachments/20190316/d9aba6d5/attachment-0001.html" target="_blank">http://lists.quantum-espresso.org/pipermail/users/attachments/20190316/d9aba6d5/attachment-0001.html</a>><br><br>------------------------------<br><br>Subject: Digest Footer<br><br>_______________________________________________<br>users mailing list<br><a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a><br><a href="https://lists.quantum-espresso.org/mailman/listinfo/users" target="_blank">https://lists.quantum-espresso.org/mailman/listinfo/users</a><br><br>------------------------------<br><br>End of users Digest, Vol 140, Issue 16<br>**************************************<br></div>
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<a href="https://lists.quantum-espresso.org/mailman/listinfo/users" rel="noreferrer" target="_blank">https://lists.quantum-espresso.org/mailman/listinfo/users</a></blockquote></div><br clear="all"><br>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div>Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,<br>Univ. Udine, via delle Scienze 208, 33100 Udine, Italy<br>Phone +39-0432-558216, fax +39-0432-558222<br><br></div></div></div></div></div>