Hi Zhen, Thanks for sending the output file.
I definitely agree with Marcos' advice on carefully checking the parameters you use for the titanium calculation. Ab initio calculations require a number of checks to make sure your total energy converges in terms of k-point mesh, basis-set, etc. After a brief scan of your output file, here are two quick suggestions: (1) Based on the output file, I would suggest switching from SZP (single zeta polarized) to DZP (double zeta polarized). SZP is usually a rather poor basis set and it could be one source of your problems. (2) The other suggestion is to do a systematic study of how your total energy (not fermi energy) changes with your k-point grid. Since titanium is a metal, you need a fine enough grid to accurately capture the Fermi surface. (3) One final note is to see if other people have investigated Ti recently using Siesta. A search on Google scholar with the terms titanium and siesta may turn up some relevant papers. Good luck, Derek > The false magnetic comes form my Ti hcp unit cell calculation. The scf > unit > cell calculation converged fine and you have see the 3*3*3 supercell > phonon > results from it. In the SCF calculation tolerance is 10e-4 and phonon is > 10e-5. The structure comes out fine. (2.80 Ang and 4.62 Ang and 90. 89.999 > 119.9722). Enclosed are the scf output file (Ti.scf.out) and force > constants > output file Ti.FC.out for 3*3*3 supercell. > > Thank you so much for working on this with me. I deeply appreciate you > time. > Best Regards > ------- > Zhen (Alex) Huang > Ph.D. Student > Nanoscale Transport Research Group > Laboratory for Computational Methods in Emerging Technologies > Cooling Technologies Research Center > School of Mechanical Engineering > Purdue University > Tel: 765 237 9733 > > > 2010/3/4 Marcos Veríssimo Alves <[email protected]> > >> Zhen, >> >> The convergence on EF is very important if you perform transport >> calculations. Otherwise, the important quantity here is the total >> energy. Now I am a bit confused by your calculations... If you are >> using such a big supercell, it could be that this huge k-point >> sampling is simply overkill and maybe your problem is not in the >> pseudopotential. Where do you get false magnetism (to quote Derek) - >> in the supercell, or in the unit cell of hcp Ti? One other thing: as >> Andrei mentioned, incomplete convergence of the SCF cycle could cause >> you to get false magnetism. What is your tolerance for the SCF >> convergence? Have you made sure that you have a fully converged SCF >> cycle, that is, that the SCF calculation ends in a number of SCF steps >> smaller than, or equal to, the maximum number of SCF steps? If >> possible, send us also the output of the calculation (the .out file). >> >> One even more basic question. For the unit cell of hcp Ti... does >> everything com out ok? I mean, structure, lattice parameters, magnetic >> moment, all come out fine for the unit cell of hcp Ti? If this is not >> the case, going to huge supercells is simply wasting time - both yours >> and the CPU time of your cluster... >> >> Marcos >> >> On Thu, Mar 4, 2010 at 6:20 PM, Zhen Huang <[email protected]> wrote: >> > Marcos- >> > Thanks for comment on it. First I took advice from previous note and >> use >> > kgrid_cutoff 25-28 Ang in recent calculation instead of k points which >> gives >> > me 18 by 18 by 11. I have increased the cutoff to 28 which gives me Ef >> > (-5.8018 eV) which is less than one percent higher energy than 25 Ang >> > (-5.8072). >> > Thanks for correcting me on the way SIESTA's calculation. I used 3*3*3 >> and >> > the 5*5*5 is running for two days already which is very slow with >> kgrid_cut >> > off 25 Ang. I am hoping the dispersion calculation will be done in >> couple >> of >> > days. As you said it could be the number of supercell can not satisfy >> the >> > require. >> > >> > Best Regards >> > ------- >> > Zhen (Alex) Huang >> > Ph.D. Student >> > Nanoscale Transport Research Group >> > Laboratory for Computational Methods in Emerging Technologies >> > Cooling Technologies Research Center >> > School of Mechanical Engineering >> > Purdue University >> > Tel: 765 237 9733 >> > >> > >> > 2010/3/4 Marcos Veríssimo Alves <[email protected]> >> >> >> >> Zhen, >> >> >> >> Again I ask you: what k-point sampling are you using in your >> >> calculations? The reason I am being pushy on this is because I am >> very >> >> familiar with an extreme case, which is graphene. You can get very >> >> reasonable results when you perform calculations for graphene with a >> >> low k-sampling, if you enforce symmetries - for example, setting >> >> >> >> LatticeConstant xxxx Ang >> >> >> >> %block LatticeVectors >> >> 0.5 0.866025404 0.0 >> >> -0.5 0.866025404 0.0 >> >> 0.0 0.0 10.0 >> >> %endblock LatticeVectors >> >> >> >> %block kgrid_monkhorst_pack >> >> 9 0 0 0.0 >> >> 0 9 0 0.0 >> >> 0 0 1 0.0 >> >> %endblock kgrid_monkhorst_pack >> >> >> >> but when you do a variable-cell calculation, in the end, you will >> find >> >> a sizeable deviation, in the angle between the in-plane lattice >> >> vectors, from the expected 60 degrees. It only goes away when you set >> >> a pretty high value for the MP grid, such as 21x21x1. Being extremely >> >> pushy, what you should do is convergence studies in your parameters, >> >> if you still haven't done so. It could well be that some parameters >> in >> >> your calculation are not good, which happens often when systematic >> >> convergence studies are not performed. Please disregard this if you >> >> have performed said studies, but contact you supervisor if you don't >> >> know how to perform one - he/she should be able to teach you how to >> do >> >> this. If not, let us know. >> >> >> >> It could be that, as Derek states, you could need semicore states or >> >> non-linear core corrections to be included in some cases. It would be >> >> advisable to check on the literature if this is the case for your >> >> metallic Ti. >> >> >> >> Now, one correction. Phonons in siesta are not calculated by >> >> frozen-phonon calculations, although siesta (and any other ab initio >> >> software, for that matter) can perform frozen-phonon calculations. >> >> What siesta does is a calculation of the force constant matrix in >> real >> >> space by finite differences. Then the phonon frequencies are >> >> calculated by diagonalization of the FC matrix. >> >> >> >> Now the following wild guess occurs to me... Your phonon softening >> >> seems to occur for large values of the phonon wavevector, q, and for >> >> small values it's pretty well-behaved. Could it be that your >> supercell >> >> is not large enough to support such a mode, and then it gives you >> this >> >> spurious softening? Phonon experts on the list, am I just guessing it >> >> wrong? >> >> >> >> Marcos >> >> >> >> >> >> On Thu, Mar 4, 2010 at 4:54 PM, Zhen Huang <[email protected]> >> wrote: >> >> > Dear Derek and folks- >> >> > Thanks for you responds. I have tried ABINIT LDA from SIESTA >> website >> and >> >> > it >> >> > also give very small lattice constants without any treatment to >> spin >> >> > (2.67 >> >> > Ang comparing to 2.95 Ang from textbook). Further, the one of the >> angles >> >> > changed from 120 to 108 degree. I could not tell what is the >> problem >> is. >> >> > I >> >> > have used PWSCF to obtain phonon dispersion of Ti before and it >> worked >> >> > out >> >> > fine. Although, I have never gone into the details of Isaev's >> paper. >> >> > The reason I switch to SIESTA, is the phonon calculation is based >> on >> >> > frozen >> >> > phonon and when it comes to large system it is much faster than >> Quantum >> >> > espresso. However, seems at this point, I am not able to get the Ti >> >> > running >> >> > properly. >> >> > Best Regards >> >> > ------- >> >> > Zhen (Alex) Huang >> >> > Ph.D. Student >> >> > Nanoscale Transport Research Group >> >> > Laboratory for Computational Methods in Emerging Technologies >> >> > Cooling Technologies Research Center >> >> > School of Mechanical Engineering >> >> > Purdue University >> >> > Tel: 765 237 9733 >> >> > >> > >> > >> > -- Derek Stewart, Ph. D. Scientific Computation Associate http://sites.google.com/site/dft4nano/ 250 Duffield Hall Cornell Nanoscale Facility (CNF) Ithaca, NY 14853 (607) 255-2856
