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: https://gitlab.com/QEF/q-e/merge_requests/378. Thank you for reporting this problem
Paolo https://gitlab.com/QEF/q-e/merge_requests/378 On Sun, Mar 17, 2019 at 11:27 AM Sylwia Golab <[email protected]> wrote: > Dear Mr Giannozzi, > > Thank you for you reply and sincerely apologize for the wrong guess I have > made. > 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: > *scf.in <http://scf.in>:* > &control > calculation='scf' > restart_mode='from_scratch', > prefix='Nb', > pseudo_dir = '/home/student3/qe/qe-6.0/pseudo/', > outdir='./tmp_dir/' > / > &system > ibrav= 3, celldm(1)=6.250946058252, nat= 1, ntyp= 1, > ecutwfc =50, ecutrho=600, > occupations="smearing", smearing="m-v", degauss=0.02 > / > &electrons > conv_thr = 1.0e-11 > mixing_beta = 0.7 > / > ATOMIC_SPECIES > Nb 92.906 Nb.pbe-spn-rrkjus_psl.1.0.0.UPF > ATOMIC_POSITIONS > Nb 0.00 0.00 0.00 > K_POINTS automatic > 4 4 4 0 0 0 > > *dos.in <http://dos.in>* > &control > calculation='nscf' > restart_mode='from_scratch', > prefix='Nb', > pseudo_dir = '/home/student3/qe/qe-6.0/pseudo/', > outdir='./tmp_dir/' > / > &system > ibrav= 3, celldm(1)=6.250946058252, nat= 1, ntyp= 1, > ecutwfc =50, ecutrho=600, > occupations="tetrahedra" > / > &electrons > conv_thr = 1.0e-11 > mixing_beta = 0.7 > / > ATOMIC_SPECIES > Nb 92.906 Nb.pbe-spn-rrkjus_psl.1.0.0.UPF > ATOMIC_POSITIONS > Nb 0.00 0.00 0.00 > K_POINTS automatic > 4 4 4 0 0 0 > > *fs.in <http://fs.in>* > &fermi > outdir='./tmp_dir/' > prefix='Nb' > / > > Firstly I am running *mpirun -np 4 pw.x <scf.in <http://scf.in> >scf.out *and > I can grep Fermi energy from *xml files: > > *[student3 qe4]$ grep fermi tmp_dir/*tmp_dir/Nb.xml: > <fermi_energy>6.529259765371975e-1</fermi_energy*> > > Then I am running *mpirun -np 4 pw.x<dos.in <http://dos.in> >dos.out *and > now I cannot see the Fermi energy in *xml*:* > *[student3 qe4]$ grep fermi tmp_dir/* (nothing appears)* > > But for sure the Fermi energy is computed in nscf cycle, because I can > grep it from dos.out file: > [student3 qe4]$ grep Fermi * > dos.out: the Fermi energy is 18.0671 ev > scf.out: the Fermi energy is 17.7670 ev > > As I mentioned before, after running *mpirun -np 4 fs.x<fs.in > <http://fs.in> >fs.out* I see in the fs.out file the line: > * 1 bands found crossing Ef = 0.000000* > > 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). > > I would like to thank you for your help in advance. > Best regards, > Sylwia > > > >>> <[email protected]> 03/16/19 12:02 PM >>> > Send users mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.quantum-espresso.org/mailman/listinfo/users > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of users digest..." > > > Today's Topics: > > 1. Negatively charged isolated molecule (Ernane de Freitas Martins) > 2. qe-6.4: problem with fs.x (Sylwia Golab) > 3. Re: Negatively charged isolated molecule (Giuseppe Mattioli) > 4. Re: Negatively charged isolated molecule > (Ernane de Freitas Martins) > 5. Re: Negatively charged isolated molecule (Michal Krompiec) > 6. Re: How to calculate water molecule energy at large cell > size? (Paolo Giannozzi) > 7. Re: qe-6.4: problem with fs.x (Paolo Giannozzi) > 8. Re: Negatively charged isolated molecule (Nattino Francesco) > 9. How can read constant velocity from input file when > restart_mode= 'restart' (=?ISO-8859-1?B?THUgSGFpbGluIA==?=) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 15 Mar 2019 13:54:49 -0300 > From: Ernane de Freitas Martins <[email protected]> > To: [email protected] > Subject: [QE-users] Negatively charged isolated molecule > Message-ID: > <cafmpbvwg4vavpshjygulpdbyhafpl7x15xfkabvguzgmeod...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > 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 > S?o Paulo, SP - Brazil > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.quantum-espresso.org/pipermail/users/attachments/20190315/17f0bf2c/attachment-0001.html > > > > ------------------------------ > > Message: 2 > Date: Fri, 15 Mar 2019 18:56:38 +0100 > From: "Sylwia Golab" <[email protected]> > To: <[email protected]> > Subject: [QE-users] qe-6.4: problem with fs.x > Message-ID: <[email protected]> > Content-Type: text/plain; charset="us-ascii" > > Dear all, > > > the program fs.x in the qe-6.4 package gives me a messages: > Message from routine pw_readschema_file: > failed retrieving input info from xml file, please check it > and: > > 1 bands found crossing Ef = 0.000000 > > so it cannot read Fermi energy. > > > > As far as I understand, the problem is, that in the 6.4 version of qe the > line > > ... > has been removed from tmp_dir/case.xml as well as from > tmp_dir/case.save/data-file-schema.xml files. > Also I cannot find any other information about Fermi energy in these *.xml > files. > > > Does anyone know how to workaround this problem? > > > > Regards,Sylwia > > > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.quantum-espresso.org/pipermail/users/attachments/20190315/881191ee/attachment-0001.html > > > > ------------------------------ > > Message: 3 > Date: Fri, 15 Mar 2019 19:04:15 +0100 > From: Giuseppe Mattioli <[email protected]> > To: [email protected] > Subject: Re: [QE-users] Negatively charged isolated molecule > Message-ID: > <20190315190415.horde.meqrst7pdvkj-9gjdjxi...@webmail.sic.rm.cnr.it> > Content-Type: text/plain; charset=utf-8; format=flowed; DelSp=Yes > > > 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 <[email protected]> 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 > > S?o 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: <[email protected]> > > > > ------------------------------ > > Message: 4 > Date: Fri, 15 Mar 2019 15:21:39 -0300 > From: Ernane de Freitas Martins <[email protected]> > To: Quantum Espresso users Forum <[email protected]> > Subject: Re: [QE-users] Negatively charged isolated molecule > Message-ID: > <CAFMPbVW75y_YnX=e=jrjb6dhs8e6bpbxk5b6twxgcrpehym...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > 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 > S?o Paulo, SP - Brazil > > Em sex, 15 de mar de 2019 15:04, Giuseppe Mattioli < > [email protected]> 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 <[email protected]> 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 > > > S?o 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: <[email protected]> > > > > _______________________________________________ > > users mailing list > > [email protected] > > https://lists.quantum-espresso.org/mailman/listinfo/users > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.quantum-espresso.org/pipermail/users/attachments/20190315/586c49b9/attachment-0001.html > > > > ------------------------------ > > Message: 5 > Date: Fri, 15 Mar 2019 18:29:16 +0000 > From: Michal Krompiec <[email protected]> > To: Quantum Espresso users Forum <[email protected]> > Subject: Re: [QE-users] Negatively charged isolated molecule > Message-ID: > <caowossp4omkammyjzpoevtq3pa2j405mpfnkgsgoqbmveot...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > 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 < > [email protected]> > 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 > > S?o Paulo, SP - Brazil > > > > Em sex, 15 de mar de 2019 15:04, Giuseppe Mattioli < > > [email protected]> 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 <[email protected]> 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 > >> > S?o 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: <[email protected]> > >> > >> _______________________________________________ > >> users mailing list > >> [email protected] > >> https://lists.quantum-espresso.org/mailman/listinfo/users > > > > _______________________________________________ > > users mailing list > > [email protected] > > https://lists.quantum-espresso.org/mailman/listinfo/users > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.quantum-espresso.org/pipermail/users/attachments/20190315/0b06d502/attachment-0001.html > > > > ------------------------------ > > Message: 6 > Date: Fri, 15 Mar 2019 22:37:45 +0100 > From: Paolo Giannozzi <[email protected]> > To: Quantum Espresso users Forum <[email protected]> > Subject: Re: [QE-users] How to calculate water molecule energy at > large cell size? > Message-ID: > <CAPMgbCs+Q7+2f_FqtmvdBSfSaHm_Ymt4fKay9ZXAVA6FVOQt=g...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > SCAN is numerically better behaved than other Meta-GGA's, but cells with a > lot of empty space are still problematic. See for instance this: > https://gitlab.com/QEF/q-e/issues/32 > > Paolo > > On Fri, Mar 15, 2019 at 1:55 AM ? ?? <[email protected]> wrote: > > > Hello, > > > > > > > > My question is how to calculate scf energy of water molecule in large > cell > > size of 12 angstrom. The energy cutoff is at 160 ry. The dft method I > used > > is scan. Mixing_beta=0.1 and diagonalization = 'cg?. When the cell size > is > > beyond 16 bohr the program reported ?too many bands are not converged and > > estimated scf accuracy is too large. > > > > > > > > I?m wondering if there is any other options I can add in my input to make > > scf energy converged for water molecule in large box? > > > > > > > > Thanks, > > > > Jing > > > > University of delaware > > > > _______________________________________________ > > users mailing list > > [email protected] > > https://lists.quantum-espresso.org/mailman/listinfo/users > > > > -- > Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.quantum-espresso.org/pipermail/users/attachments/20190315/21650365/attachment-0001.html > > > > ------------------------------ > > Message: 7 > Date: Fri, 15 Mar 2019 22:46:22 +0100 > From: Paolo Giannozzi <[email protected]> > To: Quantum Espresso users Forum <[email protected]> > Subject: Re: [QE-users] qe-6.4: problem with fs.x > Message-ID: > <capmgbctqsnf9egxjbhfpmyq4o8nrpemihxpwhg2sbv7wz9q...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > On Fri, Mar 15, 2019 at 6:57 PM Sylwia Golab <[email protected]> > wrote: > > > > > the program fs.x in the qe-6.4 package gives me a messages: > > > > * Message from routine pw_readschema_file: failed retrieving input > > info from xml file, please check it* > > > > are you using Intel v.12? it should not be a problem, the input is not > currently read from xml > > As far as I understand, the problem is, that in the 6.4 version of qe the > > line > > *<fermi_energy>...</fermi_energy>* > > has been removed from tmp_dir/case.xml > > > > I don't think so > > Also I cannot find any other information about Fermi energy in these *.xml > > files. > > > > if the Fermi energy is not in the xml files, it hasn't been computed. > > > > > Does anyone know how to workaround this problem? > > > > unlikely, without knowing exactly what you did > > Paolo > > > > > Regards, > > Sylwia > > > > > > _______________________________________________ > > users mailing list > > [email protected] > > https://lists.quantum-espresso.org/mailman/listinfo/users > > > > -- > Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.quantum-espresso.org/pipermail/users/attachments/20190315/b12e88b4/attachment-0001.html > > > > ------------------------------ > > Message: 8 > Date: Sat, 16 Mar 2019 08:02:05 +0000 > From: Nattino Francesco <[email protected]> > To: Quantum Espresso users Forum <[email protected]> > Subject: Re: [QE-users] Negatively charged isolated molecule > Message-ID: <[email protected]> > Content-Type: text/plain; charset="iso-8859-1" > > 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 <[email protected]> > 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 < > [email protected]<mailto:[email protected]>> 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 > S?o Paulo, SP - Brazil > > Em sex, 15 de mar de 2019 15:04, Giuseppe Mattioli < > [email protected]<mailto:[email protected]>> > 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 <[email protected]<mailto:[email protected]>> > 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 > > S?o 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: <[email protected]<mailto:[email protected] > >> > > _______________________________________________ > users mailing list > [email protected]<mailto:[email protected]> > https://lists.quantum-espresso.org/mailman/listinfo/users > _______________________________________________ > users mailing list > [email protected]<mailto:[email protected]> > https://lists.quantum-espresso.org/mailman/listinfo/users > > > On Mar 15, 2019 7:30 PM, Michal Krompiec <[email protected]> > 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 < > [email protected]<mailto:[email protected]>> 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 > S?o Paulo, SP - Brazil > > Em sex, 15 de mar de 2019 15:04, Giuseppe Mattioli < > [email protected]<mailto:[email protected]>> > 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 <[email protected]<mailto:[email protected]>> > 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 > > S?o 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: <[email protected]<mailto:[email protected] > >> > > _______________________________________________ > users mailing list > [email protected]<mailto:[email protected]> > https://lists.quantum-espresso.org/mailman/listinfo/users > _______________________________________________ > users mailing list > [email protected]<mailto:[email protected]> > https://lists.quantum-espresso.org/mailman/listinfo/users > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.quantum-espresso.org/pipermail/users/attachments/20190316/c5a3cd79/attachment-0001.html > > > > ------------------------------ > > Message: 9 > Date: Sat, 16 Mar 2019 17:29:07 +0800 > From: "=?ISO-8859-1?B?THUgSGFpbGluIA==?=" <[email protected]> > To: "=?ISO-8859-1?B?dXNlcnM=?=" <[email protected]> > Subject: [QE-users] How can read constant velocity from input file > when restart_mode= 'restart' > Message-ID: <[email protected]> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Paolo Giannozzi , > > > 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. > > > > 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 . > > BEWARE: works only if restart_mode='from_scratch', tested only with > electrons_dynamics='cg'. > > > 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. > > > If I have ignored something during the progress ? > > > > Any help would be appreciated. > > > > Thank you! > Best regards, > > > > ------ > > LU Hailin, Graduate Student > > State Key Laboratory of Mechanical Transmission, Chongqing University > > Chongqing 400044, China > > Tel: (+86) 18362360286 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.quantum-espresso.org/pipermail/users/attachments/20190316/d9aba6d5/attachment-0001.html > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > users mailing list > [email protected] > https://lists.quantum-espresso.org/mailman/listinfo/users > > ------------------------------ > > End of users Digest, Vol 140, Issue 16 > ************************************** > _______________________________________________ > users mailing list > [email protected] > https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. 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