[Pw_forum] something strange in rutile and anatase calculation
vega
vegalew at hotmail.com
Sun Aug 31 05:51:09 CEST 2008
> A famous example is Li which PsP was removed from PWSCF website. I met the
> same problem with K and Cs using my own pseudopotentials.
Li PsP is still on the
website,http://www.quantum-espresso.org/pseudo/1.3/html/Li.html.
Name: Lithium
Symbol: Li
Atomic number: 3
Atomic configuration: [He] 2s1
Atomic mass: 6.914 (2)
Available pseudopotentials:
Li.pz-n-vbc.UPF (details)
Perdew-Zunger (LDA) exch-corr
nonlinear core-correction
Von Barth-Car (direct fit)
Li.pbe-n-van.UPF (details)
Perdew-Burke-Ernzerhof (PBE) exch-corr
nonlinear core-correction
Vanderbilt ultrasoft
Li.pw91-n-van.UPF (details)
Perdew-Wang 91 gradient-corrected functional
nonlinear core-correction
Vanderbilt ultrasoft
vega
=================================================================================
Vega Lew (weijia liu)
PH.D Candidate in Chemical Engineering
State Key Laboratory of Materials-oriented Chemical Engineering
College of Chemistry and Chemical Engineering
Nanjing University of Technology, 210009, Nanjing, Jiangsu, China
--------------------------------------------------
From: "Eyvaz Isaev" <eyvaz_isaev at yahoo.com>
Sent: Sunday, August 31, 2008 4:19 AM
To: "vega" <vegalew at hotmail.com>
Subject: Re: [Pw_forum] something strange in rutile and anatase calculation
> --- On Sat, 8/30/08, vega <vegalew at hotmail.com> wrote:
>
>> thank you for replying
>
> Welcome.
>
>>
>> >But as far as I know sometime PsPs (not for Ti, in
>> general) fail with phonon calculations.
>>
>> Do you think there is a certain PsPs that could >calculate the lattice
>> parameters and bulk modulus correctly >but only fail with phonon
>> calculations.
>
>
>> If you find a certain PsPs fail with phonon calculations
>> what will you do next? how to adjust it?
>>
> In this case you have to generate a new PsP, if you like to deal with
> phonons. Otherwise, use what you have and what you prefer.
>
> Bests,
> Eyvaz.
> P.S. This is not a problem of the QE code. Several times I heard complains
> about PAW potentials for VASP.
>
>> vega
>>
>>
>> =================================================================================
>> Vega Lew (weijia liu)
>> PH.D Candidate in Chemical Engineering
>> State Key Laboratory of Materials-oriented Chemical
>> Engineering
>> College of Chemistry and Chemical Engineering
>> Nanjing University of Technology, 210009, Nanjing, Jiangsu,
>> China
>>
>> --------------------------------------------------
>> From: "Eyvaz Isaev" <eyvaz_isaev at yahoo.com>
>> Sent: Sunday, August 31, 2008 12:15 AM
>> To: "vega" <vegalew at hotmail.com>
>> Subject: Re: [Pw_forum] something strange in rutile and
>> anatase calculation
>>
>> > Dear Vega,
>> >
>> > --- On Sat, 8/30/08, vega <vegalew at hotmail.com>
>> wrote:
>> >
>> >> > I have read the paper and have 2 comments.
>> >>
>> >> I used to think the paper was written by you. Why
>> > did you need to read
>> >> it again?
>> >
>> > As I replied to Willy Kohn's mail, I meant reading
>> the paper from
>> > Jpn.J.Appl.Phys. Lett., he recommended, but not my own
>> paper from PNAS.
>> > So, there will be no confusing. All what I said
>> concerned only the paper
>> > and PsPs used in JpnJApplPhys.
>> >
>> > If you have done lots of calculations with the Ti
>> pseudopotential you used
>> > and got reliable results, well, it looks like to be
>> transferable. The
>> > transferability means that you can put a bare ionic
>> atom (with its PsP)
>> > into different environment, but its scattering
>> properties should be the
>> > same as for a real atom.
>> > A transferable PsP for a given atom (say Ti) should
>> work in most cases (as
>> > in your case, if you got results comparable with
>> experiments and
>> > independent methods). The way you supposed (lattice
>> parameters and bulk
>> > modulus for known phases and compounds) is correct to
>> check a PsP
>> > transferability. But as far as I know sometime PsPs
>> (not for Ti, in
>> > general) fail with phonon calculations.
>> >
>> > As references you cited support your calculations you
>> can belive your own
>> > results.
>> >
>> > Hopefully I replied briefly all questions you posted
>> in this mail.
>> >
>> > Bests,
>> > Eyvaz.
>> >
>> >
>> >> > 2. They used only LDA, but not GGA. As it is
>> well
>> >> known (hopefully I am
>> >> > not wrong here) LDA fails for the ground
>> state of Fe.
>> >> In contrast to this,
>> >> > GGA does a good job for Fe.
>> >>
>> >> But I found the sentence like this, 'The
>> generalized
>> >> gradient approximation
>> >> in the Perdew-
>> >> Burke-Ernzerhof parametrization was chosen to
>> treat the
>> >> exchange-correlation
>> >> effects.' in the Methods section. I was rather
>> >> confused.
>> >>
>> >> > So, it will be very good if Vega can
>> calculate the
>> >> total energies for the
>> >> > rutile and anatase phases in odrer to study
>> whether
>> >> their energy position
>> >> > is dependent on the choice of
>> exchange-correlation
>> >> functional.
>> >>
>> >> I used to do a little test against this. The
>> results
>> >> suggested that the GGA
>> >> overestimate the lattice parameters a little with
>> 1% and
>> >> LDA underestimate
>> >> the lattice parameters for both case. I didn't
>> pay a
>> >> lot attentions on
>> >> energy position calculated by LDA. I'll check
>> it as
>> >> soon as possible. But to
>> >> my best knowledge, there were many reports
>> suggested that
>> >> the calculated
>> >> anatase stability was better than rutile. For
>> example, J.
>> >> Chem. Phys. 126,
>> >> 154703 (2007) said 'No matter which
>> Hamiltonian or
>> >> method is used, the
>> >> results on relative stability of both phases
>> suggest that
>> >> the anatase is
>> >> more stable than the rutile phase of TiO2.'.
>> Same
>> >> conclusion also was
>> >> mentioned in Phys. Rev. B 2002, 65 (22) and Phys.
>> Rev. B
>> >> 2007, 76 et al.
>> >>
>> >> > It might also be that there is a
>> transferability
>> >> problem for these PsPs (I
>> >> > can not prove this, just suggestion).
>> >>
>> >> Because I'm a beginner for QE. I though
>> >> pseudopotentials is quite
>> >> transferable and we could use the same
>> pseudopotentials for
>> >> any mater
>> >> containing the same kind of element. For instance,
>> we could
>> >> use the same
>> >> pseudopotentials for hcp Ti, TiN, rutile,
>> brookite, anatase
>> >> and other
>> >> polymorphs under high pressure, such as
>> >> Fluorite,Baddeleyite et al. But now,
>> >> I think I'm probably wrong. Could you tell me
>> the
>> >> difference between the Ti
>> >> pseudopotentials for hcp-Ti and TiN or many
>> polymorphs of
>> >> TiO2? And I also
>> >> wonder how to judge whether the pseudopotentials
>> is
>> >> suitable for certain
>> >> calculation? to calculate the lattice parameters
>> and
>> >> compare the results
>> >> with the experimental data? Is that enough?
>> >>
>> >> > It is my pleasure that they also mentioned
>> that
>> >> including of phonon
>> >> > contribution might be important.
>> >> I would like to calculate the phonon contribution.
>> But I
>> >> have few knowledge
>> >> about it. I'll learn to do that if necessary.
>> >>
>> >> vega
>> >>
>> >>
>> >>
>> =================================================================================
>> >> Vega Lew (weijia liu)
>> >> PH.D Candidate in Chemical Engineering
>> >> State Key Laboratory of Materials-oriented
>> Chemical
>> >> Engineering
>> >> College of Chemistry and Chemical Engineering
>> >> Nanjing University of Technology, 210009, Nanjing,
>> Jiangsu,
>> >> China
>> >>
>> >> --------------------------------------------------
>> >> From: "Eyvaz Isaev"
>> <eyvaz_isaev at yahoo.com>
>> >> Sent: Saturday, August 30, 2008 7:14 AM
>> >> To: "PWSCF Forum"
>> <pw_forum at pwscf.org>
>> >> Subject: Re: [Pw_forum] something strange in
>> rutile and
>> >> anatase calculation
>> >>
>> >> > Dear Wei,
>> >> >
>> >> > Thanks a lot for bringing the paper to our
>> attention.
>> >> >
>> >> > I have read the paper and have 2 comments.
>> >> >
>> >> > 1. They used only norm-conserving
>> pseudopotentials
>> >> constructed by means of
>> >> > different methods.
>> >> >
>> >> > 2. They used only LDA, but not GGA. As it is
>> well
>> >> known (hopefully I am
>> >> > not wrong here) LDA fails for the ground
>> state of Fe.
>> >> In contrast to this,
>> >> > GGA does a good job for Fe.
>> >> >
>> >> > So, it will be very good if Vega can
>> calculate the
>> >> total energies for the
>> >> > rutile and anatase phases in odrer to study
>> whether
>> >> their energy position
>> >> > is dependent on the choice of
>> exchange-correlation
>> >> functional.
>> >> >
>> >> > It might also be that there is a
>> transferability
>> >> problem for these PsPs (I
>> >> > can not prove this, just suggestion).
>> >> >
>> >> > It is my pleasure that they also mentioned
>> that
>> >> including of phonon
>> >> > contribution might be important.
>> >> >
>> >> > Bests,
>> >> > Eyvaz.
>> >> >
>> >> >
>> >>
>> -------------------------------------------------------------------
>> >> > Prof. Eyvaz Isaev,
>> >> > Theoretical Physics Department, Moscow State
>> Institute
>> >> of Steel & Alloys,
>> >> > Russia,
>> >> > Department of Physics, Chemistry, and Biology
>> (IFM),
>> >> Linkoping University,
>> >> > Sweden
>> >> > Condensed Matter Theory Group, Uppsala
>> University,
>> >> Sweden
>> >> > Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se,
>> >> eyvaz_isaev at yahoo.com
>> >> >
>> >> >
>> >> > --- On Fri, 8/29/08, willy kohn
>> >> <willykohn at gmail.com> wrote:
>> >> >
>> >> >> From: willy kohn
>> <willykohn at gmail.com>
>> >> >> Subject: Re: [Pw_forum] something strange
>> in
>> >> rutile and anatase
>> >> >> calculation
>> >> >> To: "PWSCF Forum"
>> >> <pw_forum at pwscf.org>
>> >> >> Date: Friday, August 29, 2008, 10:02 PM
>> >> >> Hi, Vega:
>> >> >>
>> >> >> A recent result (Jpn. J. Appl. Phys. 39
>> (2000)
>> >> L847) showed
>> >> >> that different
>> >> >> pseudopotential leaded to different
>> conclusions.
>> >> >>
>> >> >> Best,
>> >> >>
>> >> >> Wei
>> >> >>
>> >> >> On Thu, Aug 28, 2008 at 4:28 AM, vega
>> >> >> <vegalew at hotmail.com> wrote:
>> >> >>
>> >> >> > Dear all,
>> >> >> >
>> >> >> > It is known that the rutile is more
>> stable
>> >> than
>> >> >> anatase in thermodynamics.
>> >> >> > Surprisingly, when I did the
>> vc-relax
>> >> calculation by
>> >> >> QE, I found
>> >> >> > the calculated energy of anatase
>> lower than
>> >> rutile.
>> >> >> Both vc-relax
>> >> >> > calculation for rutile and anatase
>> onverged
>> >> in 6 scf
>> >> >> cycles and 3 bfgs
>> >> >> > steps, giving the final enthalpy =
>> >> -362.7585836890 Ry
>> >> >> for rutile and
>> >> >> > -725.5447425835 Ry for antase. So
>> the average
>> >> energy
>> >> >> of [TiO2] unit
>> >> >> > is -181.3792918445 Ry for rutile and
>> >> -181.386185645875
>> >> >> Ry for anatase. It
>> >> >> > looks like anatase is more stable
>> than
>> >> rutile. Do you
>> >> >> think it was quite
>> >> >> > strange?
>> >> >> >
>> >> >> > To make the calculation both for
>> anatase and
>> >> rutile
>> >> >> comparable, I used the
>> >> >> > same ecutwfc=40 Ry and ecutwfc=400
>> Ry, and a
>> >> quite
>> >> >> dense k-point mesh for
>> >> >> > both case, 4x4x7 for rutile and
>> 5x5x2 for
>> >> anatase.
>> >> >> >
>> >> >> > for better understanding in my
>> calculation,
>> >> please
>> >> >> read the input file
>> >> >> > below,
>> >> >> > for anatase case,
>> >> >> > &CONTROL
>> >> >> > title =
>> 'Anatase
>> >> >> lattice' ,
>> >> >> > calculation =
>> >> 'vc-relax' ,
>> >> >> > restart_mode =
>> >> 'from_scratch'
>> >> >> ,
>> >> >> > outdir =
>> >> >> >
>> >> >>
>> >>
>> '/home/hjfeng/vega/TiO2/Anatase/lattice/vctest/tmp/'
>> >> >> ,
>> >> >> > wfcdir =
>> >> '/tmp/' ,
>> >> >> > pseudo_dir =
>> >> >>
>> '/home/hjfeng/vega/espresso-4.0/pseudo/' ,
>> >> >> > prefix =
>> 'Anatase
>> >> >> lattice' ,
>> >> >> > disk_io =
>> 'none'
>> >> ,
>> >> >> > nstep = 1000
>> ,
>> >> >> > /
>> >> >> > &SYSTEM
>> >> >> > ibrav = 6,
>> >> >> > celldm(1) =
>> 7.1356,
>> >> >> > celldm(3) =
>> 2.5122,
>> >> >> > nat = 12,
>> >> >> > ntyp = 2,
>> >> >> > ecutwfc = 40 ,
>> >> >> > ecutrho = 400 ,
>> >> >> > /
>> >> >> > &ELECTRONS
>> >> >> >
>> >> >> > /
>> >> >> > &IONS
>> >> >> > ion_dynamics =
>> 'bfgs'
>> >> ,
>> >> >> > /
>> >> >> > &CELL
>> >> >> > cell_dynamics =
>> 'bfgs'
>> >> ,
>> >> >> > /
>> >> >> > ATOMIC_SPECIES
>> >> >> > Ti 47.86700
>> Ti.pw91-sp-van_ak.UPF
>> >> >> > O 15.99940 O.pw91-van_ak.UPF
>> >> >> > ATOMIC_POSITIONS crystal
>> >> >> > Ti 0.000000000
>> 0.000000000
>> >> 0.000000000
>> >> >> > Ti 0.500000000
>> 0.500000000
>> >> 0.500000000
>> >> >> > Ti 0.000000000
>> 0.500000000
>> >> 0.250000000
>> >> >> > Ti 0.500000000
>> 0.000000000
>> >> 0.750000000
>> >> >> > O 0.000000000
>> 0.500000000
>> >> 0.042000000
>> >> >> > O 0.000000000
>> 0.000000000
>> >> 0.208000000
>> >> >> > O 0.500000000
>> 0.500000000
>> >> 0.292000000
>> >> >> > O 0.000000000
>> 0.500000000
>> >> 0.458000000
>> >> >> > O 0.500000000
>> 0.000000000
>> >> 0.542000000
>> >> >> > O 0.500000000
>> 0.500000000
>> >> 0.708000000
>> >> >> > O 0.000000000
>> 0.000000000
>> >> 0.792000000
>> >> >> > O 0.500000000
>> 1.000000000
>> >> 0.958000000
>> >> >> > K_POINTS automatic
>> >> >> > 5 5 2 1 1 1
>> >> >> >
>> >> >> > for rutile case,
>> >> >> >
>> >> >> > &CONTROL
>> >> >> > title =
>> Rutile_lattice
>> >> ,
>> >> >> > calculation =
>> >> 'vc-relax' ,
>> >> >> > restart_mode =
>> >> 'from_scratch'
>> >> >> ,
>> >> >> > outdir =
>> >> >> >
>> >>
>> '/home/vega32/TiO2/rutile/lattice/vcrelax/tmp'
>> >> >> ,
>> >> >> > wfcdir =
>> >> '/tmp/' ,
>> >> >> > pseudo_dir =
>> >> >>
>> '/home/vega32/espresso-4.0.1/pseudo/' ,
>> >> >> > prefix =
>> 'Anatase
>> >> >> lattice' ,
>> >> >> > disk_io =
>> 'none'
>> >> ,
>> >> >> > nstep = 1000
>> ,
>> >> >> > /
>> >> >> > &SYSTEM
>> >> >> > ibrav = 6,
>> >> >> > celldm(1) =
>> 8.6814,
>> >> >> > celldm(3) =
>> 0.6441,
>> >> >> > nat = 6,
>> >> >> > ntyp = 2,
>> >> >> > ecutwfc = 40 ,
>> >> >> > ecutrho = 400 ,
>> >> >> > /
>> >> >> > &ELECTRONS
>> >> >> >
>> >> >> > /
>> >> >> > &IONS
>> >> >> > ion_dynamics =
>> 'bfgs'
>> >> ,
>> >> >> > /
>> >> >> > &CELL
>> >> >> > cell_dynamics =
>> 'bfgs'
>> >> ,
>> >> >> > /
>> >> >> > ATOMIC_SPECIES
>> >> >> > O 15.99940 O.pw91-van_ak.UPF
>> >> >> > Ti 47.90000
>> Ti.pw91-sp-van_ak.UPF
>> >> >> > ATOMIC_POSITIONS crystal
>> >> >> > O 0.304800000
>> 0.304800000
>> >> 0.000000000
>> >> >> > O 0.695200000
>> 0.695200000
>> >> 0.000000000
>> >> >> > O 0.195200000
>> 0.804800000
>> >> 0.500000000
>> >> >> > O 0.804800000
>> 0.195200000
>> >> 0.500000000
>> >> >> > Ti 0.500000000
>> 0.500000000
>> >> 0.500000000
>> >> >> > Ti 0.000000000
>> 0.000000000
>> >> 0.000000000
>> >> >> > K_POINTS automatic
>> >> >> > 4 4 7 1 1 1
>> >> >> >
>> >> >> > vega
>> >> >> >
>> >> >> >
>> >> >>
>> >>
>> ==============================================================
>> >> >> > Vega Lew ( weijia liu)
>> >> >> > PH.D Candidate in Chemical
>> Engineering
>> >> >> > State Key Laboratory of
>> Materials-oriented
>> >> Chemical
>> >> >> Engineering
>> >> >> > College of Chemistry and Chemical
>> Engineering
>> >> >> > Nanjing University of Technology,
>> 210009,
>> >> Nanjing,
>> >> >> Jiangsu, China
>> >> >> >
>> >> >> >
>> >> _______________________________________________
>> >> >> > Pw_forum mailing list
>> >> >> > Pw_forum at pwscf.org
>> >> >> >
>> >> http://www.democritos.it/mailman/listinfo/pw_forum
>> >> >> >
>> >> >> >
>> >> >>
>> _______________________________________________
>> >> >> Pw_forum mailing list
>> >> >> Pw_forum at pwscf.org
>> >> >>
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>> >> >
>> >> >
>> >> >
>> >> >
>> _______________________________________________
>> >> > Pw_forum mailing list
>> >> > Pw_forum at pwscf.org
>> >> >
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>> >> >
>> >
>> >
>> >
>> >
>
>
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