On Sun, 31 Aug 2008, vega wrote: VL> > A famous example is Li which PsP was removed from PWSCF website. I met the VL> > same problem with K and Cs using my own pseudopotentials. VL> VL> Li PsP is still on the VL> website,http://www.quantum-espresso.org/pseudo/1.3/html/Li.html.
no. this was with reference to vanderbilt type lithium semi-core potentials. they are actually back on www.pwscf.org due to popular demand. those actually seem to work for phonons, provided one uses wavefunction cutoffs in the neighborhood of 200ry. getting a converged stress tensor is equally crazy, i needed 300ry for a test system recently... for the ultra-soft ones, phonons do not seem to work at all, and there are some hints that this may be true for other "tricky" elements in combination with the vanderbilt scheme. on the other hand, geometries and MD are working fine with reasonable cutoffs (85-90ry for norm conserving and 30ry for ultrasoft with density cutoff ~300ry). this is what they were created for and tested against. as you can see, testing applicability of pseudopotentials to the problem at hand is a good practice and should never be underestimated. blindly trusting existing pseudopotentials without knowing what they were used and parametrized for can easily lead to the large errors... cheers, axel. VL> Name: Lithium VL> Symbol: Li VL> Atomic number: 3 VL> Atomic configuration: [He] 2s1 VL> Atomic mass: 6.914 (2) VL> VL> Available pseudopotentials: VL> VL> Li.pz-n-vbc.UPF (details) VL> VL> Perdew-Zunger (LDA) exch-corr VL> nonlinear core-correction VL> Von Barth-Car (direct fit) VL> VL> Li.pbe-n-van.UPF (details) VL> VL> Perdew-Burke-Ernzerhof (PBE) exch-corr VL> nonlinear core-correction VL> Vanderbilt ultrasoft VL> VL> Li.pw91-n-van.UPF (details) VL> VL> Perdew-Wang 91 gradient-corrected functional VL> nonlinear core-correction VL> Vanderbilt ultrasoft VL> VL> vega VL> VL> ================================================================================= VL> Vega Lew (weijia liu) VL> PH.D Candidate in Chemical Engineering VL> State Key Laboratory of Materials-oriented Chemical Engineering VL> College of Chemistry and Chemical Engineering VL> Nanjing University of Technology, 210009, Nanjing, Jiangsu, China VL> VL> -------------------------------------------------- VL> From: "Eyvaz Isaev" <eyvaz_isaev at yahoo.com> VL> Sent: Sunday, August 31, 2008 4:19 AM VL> To: "vega" <vegalew at hotmail.com> VL> Subject: Re: [Pw_forum] something strange in rutile and anatase calculation VL> VL> > --- On Sat, 8/30/08, vega <vegalew at hotmail.com> wrote: VL> > VL> >> thank you for replying VL> > VL> > Welcome. VL> > VL> >> VL> >> >But as far as I know sometime PsPs (not for Ti, in VL> >> general) fail with phonon calculations. VL> >> VL> >> Do you think there is a certain PsPs that could >calculate the lattice VL> >> parameters and bulk modulus correctly >but only fail with phonon VL> >> calculations. VL> > VL> VL> > VL> >> If you find a certain PsPs fail with phonon calculations VL> >> what will you do next? how to adjust it? VL> >> VL> > In this case you have to generate a new PsP, if you like to deal with VL> > phonons. Otherwise, use what you have and what you prefer. VL> > VL> > Bests, VL> > Eyvaz. VL> > P.S. This is not a problem of the QE code. Several times I heard complains VL> > about PAW potentials for VASP. VL> > VL> >> vega VL> >> VL> >> VL> >> ================================================================================= VL> >> Vega Lew (weijia liu) VL> >> PH.D Candidate in Chemical Engineering VL> >> State Key Laboratory of Materials-oriented Chemical VL> >> Engineering VL> >> College of Chemistry and Chemical Engineering VL> >> Nanjing University of Technology, 210009, Nanjing, Jiangsu, VL> >> China VL> >> VL> >> -------------------------------------------------- VL> >> From: "Eyvaz Isaev" <eyvaz_isaev at yahoo.com> VL> >> Sent: Sunday, August 31, 2008 12:15 AM VL> >> To: "vega" <vegalew at hotmail.com> VL> >> Subject: Re: [Pw_forum] something strange in rutile and VL> >> anatase calculation VL> >> VL> >> > Dear Vega, VL> >> > VL> >> > --- On Sat, 8/30/08, vega <vegalew at hotmail.com> VL> >> wrote: VL> >> > VL> >> >> > I have read the paper and have 2 comments. VL> >> >> VL> >> >> I used to think the paper was written by you. Why VL> >> > did you need to read VL> >> >> it again? VL> >> > VL> >> > As I replied to Willy Kohn's mail, I meant reading VL> >> the paper from VL> >> > Jpn.J.Appl.Phys. Lett., he recommended, but not my own VL> >> paper from PNAS. VL> >> > So, there will be no confusing. All what I said VL> >> concerned only the paper VL> >> > and PsPs used in JpnJApplPhys. VL> >> > VL> >> > If you have done lots of calculations with the Ti VL> >> pseudopotential you used VL> >> > and got reliable results, well, it looks like to be VL> >> transferable. The VL> >> > transferability means that you can put a bare ionic VL> >> atom (with its PsP) VL> >> > into different environment, but its scattering VL> >> properties should be the VL> >> > same as for a real atom. VL> >> > A transferable PsP for a given atom (say Ti) should VL> >> work in most cases (as VL> >> > in your case, if you got results comparable with VL> >> experiments and VL> >> > independent methods). The way you supposed (lattice VL> >> parameters and bulk VL> >> > modulus for known phases and compounds) is correct to VL> >> check a PsP VL> >> > transferability. But as far as I know sometime PsPs VL> >> (not for Ti, in VL> >> > general) fail with phonon calculations. VL> >> > VL> >> > As references you cited support your calculations you VL> >> can belive your own VL> >> > results. VL> >> > VL> >> > Hopefully I replied briefly all questions you posted VL> >> in this mail. VL> >> > VL> >> > Bests, VL> >> > Eyvaz. VL> >> > VL> >> > VL> >> >> > 2. They used only LDA, but not GGA. As it is VL> >> well VL> >> >> known (hopefully I am VL> >> >> > not wrong here) LDA fails for the ground VL> >> state of Fe. VL> >> >> In contrast to this, VL> >> >> > GGA does a good job for Fe. VL> >> >> VL> >> >> But I found the sentence like this, 'The VL> >> generalized VL> >> >> gradient approximation VL> >> >> in the Perdew- VL> >> >> Burke-Ernzerhof parametrization was chosen to VL> >> treat the VL> >> >> exchange-correlation VL> >> >> effects.' in the Methods section. I was rather VL> >> >> confused. VL> >> >> VL> >> >> > So, it will be very good if Vega can VL> >> calculate the VL> >> >> total energies for the VL> >> >> > rutile and anatase phases in odrer to study VL> >> whether VL> >> >> their energy position VL> >> >> > is dependent on the choice of VL> >> exchange-correlation VL> >> >> functional. VL> >> >> VL> >> >> I used to do a little test against this. The VL> >> results VL> >> >> suggested that the GGA VL> >> >> overestimate the lattice parameters a little with VL> >> 1% and VL> >> >> LDA underestimate VL> >> >> the lattice parameters for both case. I didn't VL> >> pay a VL> >> >> lot attentions on VL> >> >> energy position calculated by LDA. I'll check VL> >> it as VL> >> >> soon as possible. But to VL> >> >> my best knowledge, there were many reports VL> >> suggested that VL> >> >> the calculated VL> >> >> anatase stability was better than rutile. For VL> >> example, J. VL> >> >> Chem. Phys. 126, VL> >> >> 154703 (2007) said 'No matter which VL> >> Hamiltonian or VL> >> >> method is used, the VL> >> >> results on relative stability of both phases VL> >> suggest that VL> >> >> the anatase is VL> >> >> more stable than the rutile phase of TiO2.'. VL> >> Same VL> >> >> conclusion also was VL> >> >> mentioned in Phys. Rev. B 2002, 65 (22) and Phys. VL> >> Rev. B VL> >> >> 2007, 76 et al. VL> >> >> VL> >> >> > It might also be that there is a VL> >> transferability VL> >> >> problem for these PsPs (I VL> >> >> > can not prove this, just suggestion). VL> >> >> VL> >> >> Because I'm a beginner for QE. I though VL> >> >> pseudopotentials is quite VL> >> >> transferable and we could use the same VL> >> pseudopotentials for VL> >> >> any mater VL> >> >> containing the same kind of element. For instance, VL> >> we could VL> >> >> use the same VL> >> >> pseudopotentials for hcp Ti, TiN, rutile, VL> >> brookite, anatase VL> >> >> and other VL> >> >> polymorphs under high pressure, such as VL> >> >> Fluorite,Baddeleyite et al. But now, VL> >> >> I think I'm probably wrong. Could you tell me VL> >> the VL> >> >> difference between the Ti VL> >> >> pseudopotentials for hcp-Ti and TiN or many VL> >> polymorphs of VL> >> >> TiO2? And I also VL> >> >> wonder how to judge whether the pseudopotentials VL> >> is VL> >> >> suitable for certain VL> >> >> calculation? to calculate the lattice parameters VL> >> and VL> >> >> compare the results VL> >> >> with the experimental data? Is that enough? VL> >> >> VL> >> >> > It is my pleasure that they also mentioned VL> >> that VL> >> >> including of phonon VL> >> >> > contribution might be important. VL> >> >> I would like to calculate the phonon contribution. VL> >> But I VL> >> >> have few knowledge VL> >> >> about it. I'll learn to do that if necessary. VL> >> >> VL> >> >> vega VL> >> >> VL> >> >> VL> >> >> VL> >> ================================================================================= VL> >> >> Vega Lew (weijia liu) VL> >> >> PH.D Candidate in Chemical Engineering VL> >> >> State Key Laboratory of Materials-oriented VL> >> Chemical VL> >> >> Engineering VL> >> >> College of Chemistry and Chemical Engineering VL> >> >> Nanjing University of Technology, 210009, Nanjing, VL> >> Jiangsu, VL> >> >> China VL> >> >> VL> >> >> -------------------------------------------------- VL> >> >> From: "Eyvaz Isaev" VL> >> <eyvaz_isaev at yahoo.com> VL> >> >> Sent: Saturday, August 30, 2008 7:14 AM VL> >> >> To: "PWSCF Forum" VL> >> <pw_forum at pwscf.org> VL> >> >> Subject: Re: [Pw_forum] something strange in VL> >> rutile and VL> >> >> anatase calculation VL> >> >> VL> >> >> > Dear Wei, VL> >> >> > VL> >> >> > Thanks a lot for bringing the paper to our VL> >> attention. VL> >> >> > VL> >> >> > I have read the paper and have 2 comments. VL> >> >> > VL> >> >> > 1. They used only norm-conserving VL> >> pseudopotentials VL> >> >> constructed by means of VL> >> >> > different methods. VL> >> >> > VL> >> >> > 2. They used only LDA, but not GGA. As it is VL> >> well VL> >> >> known (hopefully I am VL> >> >> > not wrong here) LDA fails for the ground VL> >> state of Fe. VL> >> >> In contrast to this, VL> >> >> > GGA does a good job for Fe. VL> >> >> > VL> >> >> > So, it will be very good if Vega can VL> >> calculate the VL> >> >> total energies for the VL> >> >> > rutile and anatase phases in odrer to study VL> >> whether VL> >> >> their energy position VL> >> >> > is dependent on the choice of VL> >> exchange-correlation VL> >> >> functional. VL> >> >> > VL> >> >> > It might also be that there is a VL> >> transferability VL> >> >> problem for these PsPs (I VL> >> >> > can not prove this, just suggestion). VL> >> >> > VL> >> >> > It is my pleasure that they also mentioned VL> >> that VL> >> >> including of phonon VL> >> >> > contribution might be important. VL> >> >> > VL> >> >> > Bests, VL> >> >> > Eyvaz. VL> >> >> > VL> >> >> > VL> >> >> VL> >> ------------------------------------------------------------------- VL> >> >> > Prof. Eyvaz Isaev, VL> >> >> > Theoretical Physics Department, Moscow State VL> >> Institute VL> >> >> of Steel & Alloys, VL> >> >> > Russia, VL> >> >> > Department of Physics, Chemistry, and Biology VL> >> (IFM), VL> >> >> Linkoping University, VL> >> >> > Sweden VL> >> >> > Condensed Matter Theory Group, Uppsala VL> >> University, VL> >> >> Sweden VL> >> >> > Eyvaz.Isaev at fysik.uu.se, isaev at ifm.liu.se, VL> >> >> eyvaz_isaev at yahoo.com VL> >> >> > VL> >> >> > VL> >> >> > --- On Fri, 8/29/08, willy kohn VL> >> >> <willykohn at gmail.com> wrote: VL> >> >> > VL> >> >> >> From: willy kohn VL> >> <willykohn at gmail.com> VL> >> >> >> Subject: Re: [Pw_forum] something strange VL> >> in VL> >> >> rutile and anatase VL> >> >> >> calculation VL> >> >> >> To: "PWSCF Forum" VL> >> >> <pw_forum at pwscf.org> VL> >> >> >> Date: Friday, August 29, 2008, 10:02 PM VL> >> >> >> Hi, Vega: VL> >> >> >> VL> >> >> >> A recent result (Jpn. J. Appl. Phys. 39 VL> >> (2000) VL> >> >> L847) showed VL> >> >> >> that different VL> >> >> >> pseudopotential leaded to different VL> >> conclusions. VL> >> >> >> VL> >> >> >> Best, VL> >> >> >> VL> >> >> >> Wei VL> >> >> >> VL> >> >> >> On Thu, Aug 28, 2008 at 4:28 AM, vega VL> >> >> >> <vegalew at hotmail.com> wrote: VL> >> >> >> VL> >> >> >> > Dear all, VL> >> >> >> > VL> >> >> >> > It is known that the rutile is more VL> >> stable VL> >> >> than VL> >> >> >> anatase in thermodynamics. VL> >> >> >> > Surprisingly, when I did the VL> >> vc-relax VL> >> >> calculation by VL> >> >> >> QE, I found VL> >> >> >> > the calculated energy of anatase VL> >> lower than VL> >> >> rutile. VL> >> >> >> Both vc-relax VL> >> >> >> > calculation for rutile and anatase VL> >> onverged VL> >> >> in 6 scf VL> >> >> >> cycles and 3 bfgs VL> >> >> >> > steps, giving the final enthalpy = VL> >> >> -362.7585836890 Ry VL> >> >> >> for rutile and VL> >> >> >> > -725.5447425835 Ry for antase. So VL> >> the average VL> >> >> energy VL> >> >> >> of [TiO2] unit VL> >> >> >> > is -181.3792918445 Ry for rutile and VL> >> >> -181.386185645875 VL> >> >> >> Ry for anatase. It VL> >> >> >> > looks like anatase is more stable VL> >> than VL> >> >> rutile. Do you VL> >> >> >> think it was quite VL> >> >> >> > strange? VL> >> >> >> > VL> >> >> >> > To make the calculation both for VL> >> anatase and VL> >> >> rutile VL> >> >> >> comparable, I used the VL> >> >> >> > same ecutwfc=40 Ry and ecutwfc=400 VL> >> Ry, and a VL> >> >> quite VL> >> >> >> dense k-point mesh for VL> >> >> >> > both case, 4x4x7 for rutile and VL> >> 5x5x2 for VL> >> >> anatase. VL> >> >> >> > VL> >> >> >> > for better understanding in my VL> >> calculation, VL> >> >> please VL> >> >> >> read the input file VL> >> >> >> > below, VL> >> >> >> > for anatase case, VL> >> >> >> > &CONTROL VL> >> >> >> > title = VL> >> 'Anatase VL> >> >> >> lattice' , VL> >> >> >> > calculation = VL> >> >> 'vc-relax' , VL> >> >> >> > restart_mode = VL> >> >> 'from_scratch' VL> >> >> >> , VL> >> >> >> > outdir = VL> >> >> >> > VL> >> >> >> VL> >> >> VL> >> '/home/hjfeng/vega/TiO2/Anatase/lattice/vctest/tmp/' VL> >> >> >> , VL> >> >> >> > wfcdir = VL> >> >> '/tmp/' , VL> >> >> >> > pseudo_dir = VL> >> >> >> VL> >> '/home/hjfeng/vega/espresso-4.0/pseudo/' , VL> >> >> >> > prefix = VL> >> 'Anatase VL> >> >> >> lattice' , VL> >> >> >> > disk_io = VL> >> 'none' VL> >> >> , VL> >> >> >> > nstep = 1000 VL> >> , VL> >> >> >> > / VL> >> >> >> > &SYSTEM VL> >> >> >> > ibrav = 6, VL> >> >> >> > celldm(1) = VL> >> 7.1356, VL> >> >> >> > celldm(3) = VL> >> 2.5122, VL> >> >> >> > nat = 12, VL> >> >> >> > ntyp = 2, VL> >> >> >> > ecutwfc = 40 , VL> >> >> >> > ecutrho = 400 , VL> >> >> >> > / VL> >> >> >> > &ELECTRONS VL> >> >> >> > VL> >> >> >> > / VL> >> >> >> > &IONS VL> >> >> >> > ion_dynamics = VL> >> 'bfgs' VL> >> >> , VL> >> >> >> > / VL> >> >> >> > &CELL VL> >> >> >> > cell_dynamics = VL> >> 'bfgs' VL> >> >> , VL> >> >> >> > / VL> >> >> >> > ATOMIC_SPECIES VL> >> >> >> > Ti 47.86700 VL> >> Ti.pw91-sp-van_ak.UPF VL> >> >> >> > O 15.99940 O.pw91-van_ak.UPF VL> >> >> >> > ATOMIC_POSITIONS crystal VL> >> >> >> > Ti 0.000000000 VL> >> 0.000000000 VL> >> >> 0.000000000 VL> >> >> >> > Ti 0.500000000 VL> >> 0.500000000 VL> >> >> 0.500000000 VL> >> >> >> > Ti 0.000000000 VL> >> 0.500000000 VL> >> >> 0.250000000 VL> >> >> >> > Ti 0.500000000 VL> >> 0.000000000 VL> >> >> 0.750000000 VL> >> >> >> > O 0.000000000 VL> >> 0.500000000 VL> >> >> 0.042000000 VL> >> >> >> > O 0.000000000 VL> >> 0.000000000 VL> >> >> 0.208000000 VL> >> >> >> > O 0.500000000 VL> >> 0.500000000 VL> >> >> 0.292000000 VL> >> >> >> > O 0.000000000 VL> >> 0.500000000 VL> >> >> 0.458000000 VL> >> >> >> > O 0.500000000 VL> >> 0.000000000 VL> >> >> 0.542000000 VL> >> >> >> > O 0.500000000 VL> >> 0.500000000 VL> >> >> 0.708000000 VL> >> >> >> > O 0.000000000 VL> >> 0.000000000 VL> >> >> 0.792000000 VL> >> >> >> > O 0.500000000 VL> >> 1.000000000 VL> >> >> 0.958000000 VL> >> >> >> > K_POINTS automatic VL> >> >> >> > 5 5 2 1 1 1 VL> >> >> >> > VL> >> >> >> > for rutile case, VL> >> >> >> > VL> >> >> >> > &CONTROL VL> >> >> >> > title = VL> >> Rutile_lattice VL> >> >> , VL> >> >> >> > calculation = VL> >> >> 'vc-relax' , VL> >> >> >> > restart_mode = VL> >> >> 'from_scratch' VL> >> >> >> , VL> >> >> >> > outdir = VL> >> >> >> > VL> >> >> VL> >> '/home/vega32/TiO2/rutile/lattice/vcrelax/tmp' VL> >> >> >> , VL> >> >> >> > wfcdir = VL> >> >> '/tmp/' , VL> >> >> >> > pseudo_dir = VL> >> >> >> VL> >> '/home/vega32/espresso-4.0.1/pseudo/' , VL> >> >> >> > prefix = VL> >> 'Anatase VL> >> >> >> lattice' , VL> >> >> >> > disk_io = VL> >> 'none' VL> >> >> , VL> >> >> >> > nstep = 1000 VL> >> , VL> >> >> >> > / VL> >> >> >> > &SYSTEM VL> >> >> >> > ibrav = 6, VL> >> >> >> > celldm(1) = VL> >> 8.6814, VL> >> >> >> > celldm(3) = VL> >> 0.6441, VL> >> >> >> > nat = 6, VL> >> >> >> > ntyp = 2, VL> >> >> >> > ecutwfc = 40 , VL> >> >> >> > ecutrho = 400 , VL> >> >> >> > / VL> >> >> >> > &ELECTRONS VL> >> >> >> > VL> >> >> >> > / VL> >> >> >> > &IONS VL> >> >> >> > ion_dynamics = VL> >> 'bfgs' VL> >> >> , VL> >> >> >> > / VL> >> >> >> > &CELL VL> >> >> >> > cell_dynamics = VL> >> 'bfgs' VL> >> >> , VL> >> >> >> > / VL> >> >> >> > ATOMIC_SPECIES VL> >> >> >> > O 15.99940 O.pw91-van_ak.UPF VL> >> >> >> > Ti 47.90000 VL> >> Ti.pw91-sp-van_ak.UPF VL> >> >> >> > ATOMIC_POSITIONS crystal VL> >> >> >> > O 0.304800000 VL> >> 0.304800000 VL> >> >> 0.000000000 VL> >> >> >> > O 0.695200000 VL> >> 0.695200000 VL> >> >> 0.000000000 VL> >> >> >> > O 0.195200000 VL> >> 0.804800000 VL> >> >> 0.500000000 VL> >> >> >> > O 0.804800000 VL> >> 0.195200000 VL> >> >> 0.500000000 VL> >> >> >> > Ti 0.500000000 VL> >> 0.500000000 VL> >> >> 0.500000000 VL> >> >> >> > Ti 0.000000000 VL> >> 0.000000000 VL> >> >> 0.000000000 VL> >> >> >> > K_POINTS automatic VL> >> >> >> > 4 4 7 1 1 1 VL> >> >> >> > VL> >> >> >> > vega VL> >> >> >> > VL> >> >> >> > VL> >> >> >> VL> >> >> VL> >> ============================================================== VL> >> >> >> > Vega Lew ( weijia liu) VL> >> >> >> > PH.D Candidate in Chemical VL> >> Engineering VL> >> >> >> > State Key Laboratory of VL> >> Materials-oriented VL> >> >> Chemical VL> >> >> >> Engineering VL> >> >> >> > College of Chemistry and Chemical VL> >> Engineering VL> >> >> >> > Nanjing University of Technology, VL> >> 210009, VL> >> >> Nanjing, VL> >> >> >> Jiangsu, China VL> >> >> >> > VL> >> >> >> > VL> >> >> _______________________________________________ VL> >> >> >> > Pw_forum mailing list VL> >> >> >> > Pw_forum at pwscf.org VL> >> >> >> > VL> >> >> http://www.democritos.it/mailman/listinfo/pw_forum VL> >> >> >> > VL> >> >> >> > VL> >> >> >> VL> >> _______________________________________________ VL> >> >> >> Pw_forum mailing list VL> >> >> >> Pw_forum at pwscf.org VL> >> >> >> VL> >> http://www.democritos.it/mailman/listinfo/pw_forum VL> >> >> > VL> >> >> > VL> >> >> > VL> >> >> > VL> >> _______________________________________________ VL> >> >> > Pw_forum mailing list VL> >> >> > Pw_forum at pwscf.org VL> >> >> > VL> >> http://www.democritos.it/mailman/listinfo/pw_forum VL> >> >> > VL> >> > VL> >> > VL> >> > VL> >> > VL> > VL> > VL> > VL> > VL> _______________________________________________ VL> Pw_forum mailing list VL> Pw_forum at pwscf.org VL> http://www.democritos.it/mailman/listinfo/pw_forum VL> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot.