Re: [Pw_forum] single atom calculations In
Thanks very much, I just presumed they were the energies for the ground state. Is there any guide on what the correct ground state energies for the pseudopotentials should be? Apart from converging the total energy in plane-wave and charge-density cutoffs in the correct magnetic state (and minimizing smearing contribution)..? Gabriel From: pw_forum-boun...@pwscf.org [pw_forum-boun...@pwscf.org] on behalf of Andrea Dal Corso [dalco...@sissa.it] Sent: Friday, May 22, 2015 5:11 PM To: pw_forum@pwscf.org Subject: Re: [Pw_forum] single atom calculations In The energy written in the pseudopotential file is the total energy of the pseudo atom in the configuration used to generate the pseudopotential not the ground state energy of the pseudo atom and pseudopotentials are generated using nonmagnetic configurations. HTH, Andrea On Thu, 2015-05-21 at 14:52 +, Gabriel Greene wrote: > Dear Espresso users, > > I want to obtain the total energy of an indium atom. In has an electronic > configuration of [Kr]4d10 5s2 5p1, so the ground state should be a doublet > due to the 1 unpaired p electron, and thus calculation of the isolated atom > should yield a magnetization of 1 Bohr Magneton. > > > After converging cutoffs and reducing smearing contribution to 0, I found > that using In.pbesol-dn-rrkjus_psl.0.2.2.UPF with the following input file I > get a total energy of -144.20595136 Ryd, whereas the value of energy > specified in this pseudopot file is -144.1890099935588 Ryd. > > If I turn off magnetization (nspin=1), I get -144.18832193 Ryd, which is > closer to the value in the pseudopot file, but not realistic in terms of the > atomic ground state (it should not be closed shell). My 1st question is why > would the calc with no magnetization yield an energy closer to the energy in > the pseudopot file, if the ground state for this atom is 1 unpaired electron? > Am I misunderstanding something about how to do magnetization in QE? > > I found basically the same behaviour at the suggested cutoffs for > In.pbesol-dn-rrkjus_psl.0.2.2.UPF (ecutwfc = 48, ecutrho = 190). > > > If I use In.pbe-d-rrkjus.UPF (convergence has also been checked, > magnetization = 1 uB), I get -136.47640747 Ryd, which is ~22 Ryd lower than > the value specified in In.pbe-d-rrkjus.UPF (-114.86650168195 Ryd). This is > quite a large discrepancy - I am wondering if there is something very wrong > in my calculations? Apologies if I am making an obvious mistake somewhere. > > > My goal is to get the correct ground state total energy for In.pz-n-bhs.UPF, > but this file does not specify the total energy, so I am first checking if I > can reproduce the correct energies for pseudopots that do specifiy the total > energy. > > > The input and output files for each case are attached, if there is any other > information I can send please let me know. > > > Thank you very much for you help, > Gabriel Greene-Diniz, > Electronics Theory Group, > Tyndall National Institute, > Cork, Ireland. > https://www.tyndall.ie/content/electronics-theory > > > > > > > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Andrea Dal CorsoTel. 0039-040-3787428 SISSA, Via Bonomea 265 Fax. 0039-040-3787249 I-34136 Trieste (Italy) e-mail: dalco...@sissa.it ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] single atom calculations In
The energy written in the pseudopotential file is the total energy of the pseudo atom in the configuration used to generate the pseudopotential not the ground state energy of the pseudo atom and pseudopotentials are generated using nonmagnetic configurations. HTH, Andrea On Thu, 2015-05-21 at 14:52 +, Gabriel Greene wrote: > Dear Espresso users, > > I want to obtain the total energy of an indium atom. In has an electronic > configuration of [Kr]4d10 5s2 5p1, so the ground state should be a doublet > due to the 1 unpaired p electron, and thus calculation of the isolated atom > should yield a magnetization of 1 Bohr Magneton. > > > After converging cutoffs and reducing smearing contribution to 0, I found > that using In.pbesol-dn-rrkjus_psl.0.2.2.UPF with the following input file I > get a total energy of -144.20595136 Ryd, whereas the value of energy > specified in this pseudopot file is -144.1890099935588 Ryd. > > If I turn off magnetization (nspin=1), I get -144.18832193 Ryd, which is > closer to the value in the pseudopot file, but not realistic in terms of the > atomic ground state (it should not be closed shell). My 1st question is why > would the calc with no magnetization yield an energy closer to the energy in > the pseudopot file, if the ground state for this atom is 1 unpaired electron? > Am I misunderstanding something about how to do magnetization in QE? > > I found basically the same behaviour at the suggested cutoffs for > In.pbesol-dn-rrkjus_psl.0.2.2.UPF (ecutwfc = 48, ecutrho = 190). > > > If I use In.pbe-d-rrkjus.UPF (convergence has also been checked, > magnetization = 1 uB), I get -136.47640747 Ryd, which is ~22 Ryd lower than > the value specified in In.pbe-d-rrkjus.UPF (-114.86650168195 Ryd). This is > quite a large discrepancy - I am wondering if there is something very wrong > in my calculations? Apologies if I am making an obvious mistake somewhere. > > > My goal is to get the correct ground state total energy for In.pz-n-bhs.UPF, > but this file does not specify the total energy, so I am first checking if I > can reproduce the correct energies for pseudopots that do specifiy the total > energy. > > > The input and output files for each case are attached, if there is any other > information I can send please let me know. > > > Thank you very much for you help, > Gabriel Greene-Diniz, > Electronics Theory Group, > Tyndall National Institute, > Cork, Ireland. > https://www.tyndall.ie/content/electronics-theory > > > > > > > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Andrea Dal CorsoTel. 0039-040-3787428 SISSA, Via Bonomea 265 Fax. 0039-040-3787249 I-34136 Trieste (Italy) e-mail: dalco...@sissa.it ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] single atom calculations In
Dear Espresso users, I want to obtain the total energy of an indium atom. In has an electronic configuration of [Kr]4d10 5s2 5p1, so the ground state should be a doublet due to the 1 unpaired p electron, and thus calculation of the isolated atom should yield a magnetization of 1 Bohr Magneton. After converging cutoffs and reducing smearing contribution to 0, I found that using In.pbesol-dn-rrkjus_psl.0.2.2.UPF with the following input file I get a total energy of -144.20595136 Ryd, whereas the value of energy specified in this pseudopot file is -144.1890099935588 Ryd. If I turn off magnetization (nspin=1), I get -144.18832193 Ryd, which is closer to the value in the pseudopot file, but not realistic in terms of the atomic ground state (it should not be closed shell). My 1st question is why would the calc with no magnetization yield an energy closer to the energy in the pseudopot file, if the ground state for this atom is 1 unpaired electron? Am I misunderstanding something about how to do magnetization in QE? I found basically the same behaviour at the suggested cutoffs for In.pbesol-dn-rrkjus_psl.0.2.2.UPF (ecutwfc = 48, ecutrho = 190). If I use In.pbe-d-rrkjus.UPF (convergence has also been checked, magnetization = 1 uB), I get -136.47640747 Ryd, which is ~22 Ryd lower than the value specified in In.pbe-d-rrkjus.UPF (-114.86650168195 Ryd). This is quite a large discrepancy - I am wondering if there is something very wrong in my calculations? Apologies if I am making an obvious mistake somewhere. My goal is to get the correct ground state total energy for In.pz-n-bhs.UPF, but this file does not specify the total energy, so I am first checking if I can reproduce the correct energies for pseudopots that do specifiy the total energy. The input and output files for each case are attached, if there is any other information I can send please let me know. Thank you very much for you help, Gabriel Greene-Diniz, Electronics Theory Group, Tyndall National Institute, Cork, Ireland. https://www.tyndall.ie/content/electronics-theory In_pbesol_mag.in Description: In_pbesol_mag.in In_pbesol_mag.out Description: In_pbesol_mag.out In_pbesol_nomag.in Description: In_pbesol_nomag.in In_pbesol_nomag.out Description: In_pbesol_nomag.out In.pbe-d-rrkjus.in Description: In.pbe-d-rrkjus.in In.pbe-d-rrkjus.out Description: In.pbe-d-rrkjus.out ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] single atom calculations
?Thank you for your response. Adib Samin Graduate Fellow The Ohio State University From: pw_forum-bounces at pwscf.org on behalf of Arles V. Gil Rebaza <arvi...@gmail.com> Sent: Monday, July 14, 2014 6:28 PM To: PWSCF Forum Subject: Re: [Pw_forum] single atom calculations Dear Adib Is it possible to use Quantum Espresso to calculate the properties of a single atom from a certain element? yes It is my understanding that periodic boundary conditions need to be imposed. Would it be possible to create a sufficiently large unit cell containing a single atom of the desired element? Yes, you must to use an enough big cubic cell, and may be you should read the tag "assume_isolated" in the QE manual. Best PhD. Arles V. Gil Rebaza IFLP - Argentina 2014-07-14 19:01 GMT-03:00 Samin, Adib J. mailto:samin.2 at buckeyemail.osu.edu>>: ?Dear Quantum Espresso users, Is it possible to use Quantum Espresso to calculate the properties of a single atom from a certain element? It is my understanding that periodic boundary conditions need to be imposed. Would it be possible to create a sufficiently large unit cell containing a single atom of the desired element? Any clarifications on this issue would be greatly appreciated. Thanks, Adib Samin Adib Samin Graduate Fellow The Department of Aerospace and Mechanical Engineering The Ohio State University ___ Pw_forum mailing list Pw_forum at pwscf.org<mailto:Pw_forum at pwscf.org> http://pwscf.org/mailman/listinfo/pw_forum -- ###-> Arles V. <-### -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140715/83c35962/attachment.html
[Pw_forum] single atom calculations
Dear Adib
please try to learn the following example about atomic oxygen and not bad
to apply it to other atoms and compare the result with your
general chemistry comprehension.
calculation='scf',
restart_mode='restart',
prefix='O',
pseudo_dir = '../../pseudo/',
outdir='../tmp/',
/
ibrav= 0, celldm(1)=2.7585, nat= 1, ntyp= 1,
ecutwfc = 40, ecutrho = 400, nspin=2, starting_magnetization=1,
occupations='smearing', smearing='marzari-vanderbilt', degauss=0.001,
/
conv_thr = 1.0d-8,
mixing_beta=0.3,
electron_maxstep=200
/
CELL_PARAMETERS
10. 0. 0.
0.0 10.000 0.
0. 0. 10.000
ATOMIC_SPECIES
O 15.9994 O.pbe-rrkjus.UPF
ATOMIC_POSITIONS {alat}
O0.0 0.0 0.0
K_POINTS {gamma}
Best Wishes, m
Masoud Nahali
SUT
masoud.nahali at gmail.com
alum.sharif.edu/~m_nahali
On Tue, Jul 15, 2014 at 2:31 AM, Samin, Adib J. wrote:
> Dear Quantum Espresso users,
>
>
> Is it possible to use Quantum Espresso to calculate the properties of a
> single atom from a certain element?
>
> It is my understanding that periodic boundary conditions need to be
> imposed.
>
> Would it be possible to create a sufficiently large unit cell containing a
> single atom of the desired element?
>
> Any clarifications on this issue would be greatly appreciated.
>
>
> Thanks,
>
> Adib Samin
>
>
> Adib Samin
>
> Graduate Fellow
>
> The Department of Aerospace and Mechanical Engineering
>
> The Ohio State University
>
>
>
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
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[Pw_forum] single atom calculations
?Dear Quantum Espresso users, Is it possible to use Quantum Espresso to calculate the properties of a single atom from a certain element? It is my understanding that periodic boundary conditions need to be imposed. Would it be possible to create a sufficiently large unit cell containing a single atom of the desired element? Any clarifications on this issue would be greatly appreciated. Thanks, Adib Samin Adib Samin Graduate Fellow The Department of Aerospace and Mechanical Engineering The Ohio State University -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140714/9828b67f/attachment.html
[Pw_forum] single atom calculations
Dear Adib Is it possible to use Quantum Espresso to calculate the properties of a single atom from a certain element? yes It is my understanding that periodic boundary conditions need to be imposed. Would it be possible to create a sufficiently large unit cell containing a single atom of the desired element? Yes, you must to use an enough big cubic cell, and may be you should read the tag "assume_isolated" in the QE manual. Best PhD. Arles V. Gil Rebaza IFLP - Argentina 2014-07-14 19:01 GMT-03:00 Samin, Adib J. : > ?Dear Quantum Espresso users, > > > Is it possible to use Quantum Espresso to calculate the properties of a > single atom from a certain element? > > It is my understanding that periodic boundary conditions need to be > imposed. > > Would it be possible to create a sufficiently large unit cell containing a > single atom of the desired element? > > Any clarifications on this issue would be greatly appreciated. > > > Thanks, > > Adib Samin > > > Adib Samin > > Graduate Fellow > > The Department of Aerospace and Mechanical Engineering > > The Ohio State University > > > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- ###-> Arles V. <-### -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140714/9ffd1f3a/attachment.html
