[QE-users] qe-6.4: problem with fs.x
Paolo Giannozzi
p.giannozzi at gmail.com
Mon Mar 18 14:47:32 CET 2019
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 <Sylwia.Golab at fis.agh.edu.pl>
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
>
>
> >>> <users-request at lists.quantum-espresso.org> 03/16/19 12:02 PM >>>
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> 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 <ernanefmg at gmail.com>
> To: users at lists.quantum-espresso.org
> Subject: [QE-users] Negatively charged isolated molecule
> Message-ID:
> <CAFMPbVWG4VAvpsHjyGULPdbyhafpL7X15xfKAbVGuZgMEoDimA at 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
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> ------------------------------
>
> Message: 2
> Date: Fri, 15 Mar 2019 18:56:38 +0100
> From: "Sylwia Golab" <Sylwia.Golab at fis.agh.edu.pl>
> To: <users at lists.quantum-espresso.org>
> Subject: [QE-users] qe-6.4: problem with fs.x
> Message-ID: <5C8BF566020000D400029CFA at orion.fis.agh.edu.pl>
> 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
>
>
>
>
>
>
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> ------------------------------
>
> Message: 3
> Date: Fri, 15 Mar 2019 19:04:15 +0100
> From: Giuseppe Mattioli <giuseppe.mattioli at ism.cnr.it>
> To: users at lists.quantum-espresso.org
> Subject: Re: [QE-users] Negatively charged isolated molecule
> Message-ID:
> <20190315190415.Horde.meqRST7PDvkj-9gJDJxiN7w at 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 <ernanefmg at gmail.com> ha scritto:
>
> > Hello,
> >
> > I'm experiencing a problem to run a negatively charge molecule in quantum
> > espresso. The system is CO32-.
> >
> > I try both vacuum and solvated (environ) calculations. The solvated one
> > works fine.
> >
> > The problem is the calculation in vacuum. It never give the first ionic
> > step because the SCF accuracy never reaches the convence criterion.
> >
> > I tried many different solutions (increase cutoffs and box size, use
> assume
> > isolated, decreasing and changing the mixing scheme and etc) and nothing
> > works.
> >
> > The unique calculation that works fine for vacuum is the one with a box
> > size of 7.9 x 7.9 x 7.9 A. I really don't understand why it only works
> for
> > this specific box size.
> >
> > I ran several other charged systems (+1, +2 and -1 total charge) and all
> of
> > them worked fine. The problem appears for -2 total charge in vacuum.
> >
> > Would some of you kindly help me in this?
> >
> > Cheers,
> >
> > Dr. Ernane de Freitas Martins
> > Postdoctoral researcher
> > IF - USP
> > 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: <giuseppe.mattioli at ism.cnr.it>
>
>
>
> ------------------------------
>
> Message: 4
> Date: Fri, 15 Mar 2019 15:21:39 -0300
> From: Ernane de Freitas Martins <ernanefmg at gmail.com>
> To: Quantum Espresso users Forum <users at lists.quantum-espresso.org>
> Subject: Re: [QE-users] Negatively charged isolated molecule
> Message-ID:
> <CAFMPbVW75y_YnX=e=JrjB6Dhs8E6bpbxk5b6twxgcRpehYme4Q at 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 <
> giuseppe.mattioli at ism.cnr.it> escreveu:
>
> >
> > Dear Ernane
> > Your question contains part of the answer! Carbonate ion (CO3 2-) is
> > not stable outside water, and calculations of its properties in gas
> > phase are likely not so meaningful, but in the case of model
> > thermodynamics cycles (e.g. Born-Haber). The excess negative charge is
> > unbound when not stabilized by a strongly polar solvent, and this is
> > likely responsible for instabilities in the construction of the
> > Kohn-Sham potential along scf iterations. Moreover, this happens on
> > top of the strong delocalization error you experience when you use a
> > standard GGA exchange-correlation functional, when the
> > self-interaction of strongly localized electrons in the J[n] Coulomb
> > potential is not cancelled by a same term in the semi local exchange
> > potential. You may minimize this latter source of error by using a
> > hybrid GGA-EXX functional such as B3LYP, where the non local
> > Hartree-Fock part of the exchange functional can recover part of the
> > delocalization error, but you are not free yet from the instability of
> > carbonate in gas phase.
> > HTH
> > Giuseppe
> >
> > Ernane de Freitas Martins <ernanefmg at gmail.com> ha scritto:
> >
> > > Hello,
> > >
> > > I'm experiencing a problem to run a negatively charge molecule in
> quantum
> > > espresso. The system is CO32-.
> > >
> > > I try both vacuum and solvated (environ) calculations. The solvated one
> > > works fine.
> > >
> > > The problem is the calculation in vacuum. It never give the first ionic
> > > step because the SCF accuracy never reaches the convence criterion.
> > >
> > > I tried many different solutions (increase cutoffs and box size, use
> > assume
> > > isolated, decreasing and changing the mixing scheme and etc) and
> nothing
> > > works.
> > >
> > > The unique calculation that works fine for vacuum is the one with a box
> > > size of 7.9 x 7.9 x 7.9 A. I really don't understand why it only works
> > for
> > > this specific box size.
> > >
> > > I ran several other charged systems (+1, +2 and -1 total charge) and
> all
> > of
> > > them worked fine. The problem appears for -2 total charge in vacuum.
> > >
> > > Would some of you kindly help me in this?
> > >
> > > Cheers,
> > >
> > > Dr. Ernane de Freitas Martins
> > > Postdoctoral researcher
> > > IF - USP
> > > 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: <giuseppe.mattioli at ism.cnr.it>
> >
> > _______________________________________________
> > users mailing list
> > users at lists.quantum-espresso.org
> > https://lists.quantum-espresso.org/mailman/listinfo/users
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> ------------------------------
>
> Message: 5
> Date: Fri, 15 Mar 2019 18:29:16 +0000
> From: Michal Krompiec <michal.krompiec at gmail.com>
> To: Quantum Espresso users Forum <users at lists.quantum-espresso.org>
> Subject: Re: [QE-users] Negatively charged isolated molecule
> Message-ID:
> <CAOWoSSP4oMKAmMyJzpoEVtQ3pa2j405MPFNKgSGOQbMVeOTr0A at 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 <
> ernanefmg at gmail.com>
> wrote:
>
> > Dear Giuseppe,
> >
> > I really appreciate your answer. Thank you very much for using your time
> > to answer my question.
> >
> > I'll think on your suggestion about trying hybrid functionals. The point
> > is that I need to estimate the solvation energy for carbonate ion using
> the
> > environ module, then I'll need to run a vacuum calculation using the same
> > functional I'm already using rVV-10).
> >
> > Thank you again for replying.
> >
> > Atenciosamente,
> >
> >
> > Dr. Ernane de Freitas Martins
> > Postdoctoral researcher
> > IF - USP
> > S?o Paulo, SP - Brazil
> >
> > Em sex, 15 de mar de 2019 15:04, Giuseppe Mattioli <
> > giuseppe.mattioli at ism.cnr.it> escreveu:
> >
> >>
> >> Dear Ernane
> >> Your question contains part of the answer! Carbonate ion (CO3 2-) is
> >> not stable outside water, and calculations of its properties in gas
> >> phase are likely not so meaningful, but in the case of model
> >> thermodynamics cycles (e.g. Born-Haber). The excess negative charge is
> >> unbound when not stabilized by a strongly polar solvent, and this is
> >> likely responsible for instabilities in the construction of the
> >> Kohn-Sham potential along scf iterations. Moreover, this happens on
> >> top of the strong delocalization error you experience when you use a
> >> standard GGA exchange-correlation functional, when the
> >> self-interaction of strongly localized electrons in the J[n] Coulomb
> >> potential is not cancelled by a same term in the semi local exchange
> >> potential. You may minimize this latter source of error by using a
> >> hybrid GGA-EXX functional such as B3LYP, where the non local
> >> Hartree-Fock part of the exchange functional can recover part of the
> >> delocalization error, but you are not free yet from the instability of
> >> carbonate in gas phase.
> >> HTH
> >> Giuseppe
> >>
> >> Ernane de Freitas Martins <ernanefmg at gmail.com> ha scritto:
> >>
> >> > Hello,
> >> >
> >> > I'm experiencing a problem to run a negatively charge molecule in
> >> quantum
> >> > espresso. The system is CO32-.
> >> >
> >> > I try both vacuum and solvated (environ) calculations. The solvated
> one
> >> > works fine.
> >> >
> >> > The problem is the calculation in vacuum. It never give the first
> ionic
> >> > step because the SCF accuracy never reaches the convence criterion.
> >> >
> >> > I tried many different solutions (increase cutoffs and box size, use
> >> assume
> >> > isolated, decreasing and changing the mixing scheme and etc) and
> nothing
> >> > works.
> >> >
> >> > The unique calculation that works fine for vacuum is the one with a
> box
> >> > size of 7.9 x 7.9 x 7.9 A. I really don't understand why it only works
> >> for
> >> > this specific box size.
> >> >
> >> > I ran several other charged systems (+1, +2 and -1 total charge) and
> >> all of
> >> > them worked fine. The problem appears for -2 total charge in vacuum.
> >> >
> >> > Would some of you kindly help me in this?
> >> >
> >> > Cheers,
> >> >
> >> > Dr. Ernane de Freitas Martins
> >> > Postdoctoral researcher
> >> > IF - USP
> >> > 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: <giuseppe.mattioli at ism.cnr.it>
> >>
> >> _______________________________________________
> >> users mailing list
> >> users at lists.quantum-espresso.org
> >> https://lists.quantum-espresso.org/mailman/listinfo/users
> >
> > _______________________________________________
> > users mailing list
> > users at lists.quantum-espresso.org
> > https://lists.quantum-espresso.org/mailman/listinfo/users
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> ------------------------------
>
> Message: 6
> Date: Fri, 15 Mar 2019 22:37:45 +0100
> From: Paolo Giannozzi <p.giannozzi at gmail.com>
> To: Quantum Espresso users Forum <users at lists.quantum-espresso.org>
> Subject: Re: [QE-users] How to calculate water molecule energy at
> large cell size?
> Message-ID:
> <CAPMgbCs+Q7+2f_FqtmvdBSfSaHm_Ymt4fKay9ZXAVA6FVOQt=g at 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 ? ?? <alingjing at outlook.com> 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
> > users at lists.quantum-espresso.org
> > 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
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> ------------------------------
>
> Message: 7
> Date: Fri, 15 Mar 2019 22:46:22 +0100
> From: Paolo Giannozzi <p.giannozzi at gmail.com>
> To: Quantum Espresso users Forum <users at lists.quantum-espresso.org>
> Subject: Re: [QE-users] qe-6.4: problem with fs.x
> Message-ID:
> <CAPMgbCtQSnF9eGXJbhFPMyQ4o8nRpemiHXPWhG2sbv7Wz9q47Q at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> On Fri, Mar 15, 2019 at 6:57 PM Sylwia Golab <Sylwia.Golab at fis.agh.edu.pl>
> 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
> > users at lists.quantum-espresso.org
> > 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
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>
> Message: 8
> Date: Sat, 16 Mar 2019 08:02:05 +0000
> From: Nattino Francesco <francesco.nattino at epfl.ch>
> To: Quantum Espresso users Forum <users at lists.quantum-espresso.org>
> Subject: Re: [QE-users] Negatively charged isolated molecule
> Message-ID: <5459c922-ff5d-4de0-a4cc-32e935d1efd3 at email.android.com>
> 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 <michal.krompiec at gmail.com>
> wrote:
> Dear Ernane,
> Have you thought of using a more sophisticated method (like GW) on [CO3]-
> to calculate its EA? This would give you the energy of [CO3]2- in vacuum.
> Best,
> Michal Krompiec
> University of Southampton & Merck KGaA
>
> On Fri, 15 Mar 2019 at 18:22, Ernane de Freitas Martins <
> ernanefmg at gmail.com<mailto:ernanefmg at gmail.com>> wrote:
> Dear Giuseppe,
>
> I really appreciate your answer. Thank you very much for using your time
> to answer my question.
>
> I'll think on your suggestion about trying hybrid functionals. The point
> is that I need to estimate the solvation energy for carbonate ion using the
> environ module, then I'll need to run a vacuum calculation using the same
> functional I'm already using rVV-10).
>
> Thank you again for replying.
>
> Atenciosamente,
>
>
> Dr. Ernane de Freitas Martins
> Postdoctoral researcher
> IF - USP
> S?o Paulo, SP - Brazil
>
> Em sex, 15 de mar de 2019 15:04, Giuseppe Mattioli <
> giuseppe.mattioli at ism.cnr.it<mailto:giuseppe.mattioli at ism.cnr.it>>
> escreveu:
>
> Dear Ernane
> Your question contains part of the answer! Carbonate ion (CO3 2-) is
> not stable outside water, and calculations of its properties in gas
> phase are likely not so meaningful, but in the case of model
> thermodynamics cycles (e.g. Born-Haber). The excess negative charge is
> unbound when not stabilized by a strongly polar solvent, and this is
> likely responsible for instabilities in the construction of the
> Kohn-Sham potential along scf iterations. Moreover, this happens on
> top of the strong delocalization error you experience when you use a
> standard GGA exchange-correlation functional, when the
> self-interaction of strongly localized electrons in the J[n] Coulomb
> potential is not cancelled by a same term in the semi local exchange
> potential. You may minimize this latter source of error by using a
> hybrid GGA-EXX functional such as B3LYP, where the non local
> Hartree-Fock part of the exchange functional can recover part of the
> delocalization error, but you are not free yet from the instability of
> carbonate in gas phase.
> HTH
> Giuseppe
>
> Ernane de Freitas Martins <ernanefmg at gmail.com<mailto:ernanefmg at gmail.com>>
> ha scritto:
>
> > Hello,
> >
> > I'm experiencing a problem to run a negatively charge molecule in quantum
> > espresso. The system is CO32-.
> >
> > I try both vacuum and solvated (environ) calculations. The solvated one
> > works fine.
> >
> > The problem is the calculation in vacuum. It never give the first ionic
> > step because the SCF accuracy never reaches the convence criterion.
> >
> > I tried many different solutions (increase cutoffs and box size, use
> assume
> > isolated, decreasing and changing the mixing scheme and etc) and nothing
> > works.
> >
> > The unique calculation that works fine for vacuum is the one with a box
> > size of 7.9 x 7.9 x 7.9 A. I really don't understand why it only works
> for
> > this specific box size.
> >
> > I ran several other charged systems (+1, +2 and -1 total charge) and all
> of
> > them worked fine. The problem appears for -2 total charge in vacuum.
> >
> > Would some of you kindly help me in this?
> >
> > Cheers,
> >
> > Dr. Ernane de Freitas Martins
> > Postdoctoral researcher
> > IF - USP
> > 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: <giuseppe.mattioli at ism.cnr.it<mailto:giuseppe.mattioli at ism.cnr.it
> >>
>
> _______________________________________________
> users mailing list
> users at lists.quantum-espresso.org<mailto:users at lists.quantum-espresso.org>
> https://lists.quantum-espresso.org/mailman/listinfo/users
> _______________________________________________
> users mailing list
> users at lists.quantum-espresso.org<mailto:users at lists.quantum-espresso.org>
> https://lists.quantum-espresso.org/mailman/listinfo/users
>
>
> On Mar 15, 2019 7:30 PM, Michal Krompiec <michal.krompiec at gmail.com>
> wrote:
> Dear Ernane,
> Have you thought of using a more sophisticated method (like GW) on [CO3]-
> to calculate its EA? This would give you the energy of [CO3]2- in vacuum.
> Best,
> Michal Krompiec
> University of Southampton & Merck KGaA
>
> On Fri, 15 Mar 2019 at 18:22, Ernane de Freitas Martins <
> ernanefmg at gmail.com<mailto:ernanefmg at gmail.com>> wrote:
> Dear Giuseppe,
>
> I really appreciate your answer. Thank you very much for using your time
> to answer my question.
>
> I'll think on your suggestion about trying hybrid functionals. The point
> is that I need to estimate the solvation energy for carbonate ion using the
> environ module, then I'll need to run a vacuum calculation using the same
> functional I'm already using rVV-10).
>
> Thank you again for replying.
>
> Atenciosamente,
>
>
> Dr. Ernane de Freitas Martins
> Postdoctoral researcher
> IF - USP
> S?o Paulo, SP - Brazil
>
> Em sex, 15 de mar de 2019 15:04, Giuseppe Mattioli <
> giuseppe.mattioli at ism.cnr.it<mailto:giuseppe.mattioli at ism.cnr.it>>
> escreveu:
>
> Dear Ernane
> Your question contains part of the answer! Carbonate ion (CO3 2-) is
> not stable outside water, and calculations of its properties in gas
> phase are likely not so meaningful, but in the case of model
> thermodynamics cycles (e.g. Born-Haber). The excess negative charge is
> unbound when not stabilized by a strongly polar solvent, and this is
> likely responsible for instabilities in the construction of the
> Kohn-Sham potential along scf iterations. Moreover, this happens on
> top of the strong delocalization error you experience when you use a
> standard GGA exchange-correlation functional, when the
> self-interaction of strongly localized electrons in the J[n] Coulomb
> potential is not cancelled by a same term in the semi local exchange
> potential. You may minimize this latter source of error by using a
> hybrid GGA-EXX functional such as B3LYP, where the non local
> Hartree-Fock part of the exchange functional can recover part of the
> delocalization error, but you are not free yet from the instability of
> carbonate in gas phase.
> HTH
> Giuseppe
>
> Ernane de Freitas Martins <ernanefmg at gmail.com<mailto:ernanefmg at gmail.com>>
> ha scritto:
>
> > Hello,
> >
> > I'm experiencing a problem to run a negatively charge molecule in quantum
> > espresso. The system is CO32-.
> >
> > I try both vacuum and solvated (environ) calculations. The solvated one
> > works fine.
> >
> > The problem is the calculation in vacuum. It never give the first ionic
> > step because the SCF accuracy never reaches the convence criterion.
> >
> > I tried many different solutions (increase cutoffs and box size, use
> assume
> > isolated, decreasing and changing the mixing scheme and etc) and nothing
> > works.
> >
> > The unique calculation that works fine for vacuum is the one with a box
> > size of 7.9 x 7.9 x 7.9 A. I really don't understand why it only works
> for
> > this specific box size.
> >
> > I ran several other charged systems (+1, +2 and -1 total charge) and all
> of
> > them worked fine. The problem appears for -2 total charge in vacuum.
> >
> > Would some of you kindly help me in this?
> >
> > Cheers,
> >
> > Dr. Ernane de Freitas Martins
> > Postdoctoral researcher
> > IF - USP
> > 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: <giuseppe.mattioli at ism.cnr.it<mailto:giuseppe.mattioli at ism.cnr.it
> >>
>
> _______________________________________________
> users mailing list
> users at lists.quantum-espresso.org<mailto:users at lists.quantum-espresso.org>
> https://lists.quantum-espresso.org/mailman/listinfo/users
> _______________________________________________
> users mailing list
> users at lists.quantum-espresso.org<mailto:users at lists.quantum-espresso.org>
> https://lists.quantum-espresso.org/mailman/listinfo/users
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> ------------------------------
>
> Message: 9
> Date: Sat, 16 Mar 2019 17:29:07 +0800
> From: "=?ISO-8859-1?B?THUgSGFpbGluIA==?=" <415005271 at qq.com>
> To: "=?ISO-8859-1?B?dXNlcnM=?=" <users at lists.quantum-espresso.org>
> Subject: [QE-users] How can read constant velocity from input file
> when restart_mode= 'restart'
> Message-ID: <tencent_73D1D71A3787D2E58285BFC014DBEE84C206 at qq.com>
> 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
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>
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--
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
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