Dear Akbar, As to possible relation between band structure calculation and dipole moment, that was my desperate assumption how to reconcile the contradiction between symmetry and my current results. I think, they are not connected (anyhow).
Best, Artem Baskin, PhD student, University of Illinois at Chicago On Fri, March 19, 2010 5:39 am, akbar jahangiri wrote: > Dear Artem > > Regarding this sentence, i have a question . Are they connected through > plan-wave method ? if yes why? > >>>" and structure calculations and dipole moment are > separated things (if only they are not connected somehow through > plane-wave method). " > > Best regards > Akbar jahangiri > > 2010/3/16 Marcos Veríssimo Alves <[email protected]> > >> About the coordinates, I haven't really checked them. If they are >> incorrect then it would be the most obvious source of error. >> >> For the dipole moment, I don't see how the origin of coordinates and >> k-point sampling could possibly be related. Surely you are right, the >> dipole moment is independent of the origin of coordinates, but the >> origin of coordinates and the k-point sampling are ultimately >> completely un-related to each other. The issue with k-point sampling >> is that it is used for performing a sum over the energies of occupied >> bands in k-space, which accounts for the part of the total energy. If >> this is wrong, then your total energy is wrong as well. If your total >> energy is wrong, then by the Kohn-Sham theorems you have a wrong >> charge density distribution. And, if you have a wrong charge density >> distribution, then definitely your dipole moment would be wrong. >> Fundamentally, this is it. >> >> Nevertheless, as it has been discussed rather recently in the list, >> bear in mind that, in a solid, the dipole would be ill-defined, and to >> get a meaningful value you'd need to resort to the Berry's phase >> approximation. So, it would be advisable (1) to check your initial >> coordinates just in case and (2) see if you get the dipole moment to >> converge with an increasing number of k-points along the ribbon's >> length. >> >> Cheers, >> >> Marcos >> >> >> On Tue, Mar 16, 2010 at 12:22 PM, Roland Gillen >> <[email protected]> wrote: >> > Artem, >> > >> > I might be terribly wrong mistaken, but your geometry doesn't look >> like >> it's >> > symmetric. Look at the y-coordinates of your H-atoms. They are about >> +5.8 >> > and -5.8. >> > Your left-most carbon atoms are at y=-4.9, but the carbon atoms at the >> other >> > edge are at y=7.3. >> > Btw. the x-positions of the hydrogen atoms don't seem reasonable as >> well. >> > >> > Maybe that is the reason for your wrong band structures? >> > >> > Cheers >> > Roland >> > >> > [email protected] schrieb: >> >> >> >> Thank you, Marcos, for such a quick response. >> >> >> >> You are absolutely right about the low level of mesh cutoff that I >> used, >> I >> >> used it on purpose to cut down on the calculation time. But there is >> a >> >> thing that I still don't understand in your explanations: how may any >> >> k-point sampling be related with calculation of dipole moment of my >> >> system? Dipole moment is invariant (with respect of the used system >> of >> >> coordinates) for electrically neutral system, therefore it should not >> >> depend on the lattice vector determination and, consequently, on any >> >> k-point sampling. >> >> Is it?. Moreover, band structure calculations and dipole moment are >> >> separated things (if only they are not connected somehow through >> >> plane-wave method). So, I can understand why the magnitude of >> non-zero >> >> dipole moment may vary depending on the mesh cutoff value, but zero >> should >> >> be equal zero. >> >> The question about dipole moment is important for me because I look >> for >> >> the reasons which result in errors of my band structure calculation >> for >> >> graphene ribbon. (Initially I thought that there was something wrong >> with >> >> my input file information or something like this). >> >> >> >> Thank you once again, hope you will help me with that weird thing. >> >> >> >> Artem Baskin, >> >> PhD student, >> >> University of Illinois at Chicago >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >>> >> >>> Artem, >> >>> >> >>> Two things could be hindering your calculation. First, your mesh >> >>> cutoff is quite low. I would use at least 200 Ry to get only decent >> >>> results. In my experience with 300 Ry you get pretty good results >> for >> >>> a graphitic system. Second, I don't see any k-point sampling along >> the >> >>> ribbon length. This definitely could be the cause of your >> fluctuating >> >>> dipole value. >> >>> >> >>> Cheers, >> >>> >> >>> Marcos >> >>> >> >>> On Sat, Mar 13, 2010 at 3:08 AM, [email protected] <[email protected]> >> wrote: >> >>> >> >>>> >> >>>> Hi all! >> >>>> I am a new user of Siesta and I'm involved in graphene band >> structure >> >>>> calculations. I can not obtain the correct band structure for a >> graphene >> >>>> nanoribon (N=3m+2, armchair passivated by H-atoms). Trying to do >> that >> I >> >>>> was overwhelmed with the fact that the system absolutely >> symmetrical >> in >> >>>> Y-axis (finite size, 5 honeycomb rings) has non-zero dipole moment >> along >> >>>> Y-axix which depends sharply on the Meshcutoff value. >> >>>> Could anyone explain me where it comes from? What are the possible >> >>>> sources >> >>>> of this "effect" and how it may affect the band structure? >> >>>> >> >>>> The replica of my .fdf and .out files are attached below. >> >>>> >> >>>> Thanks for any reasonable help. >> >>>> >> >>>> From input-file >> >>>> >> >>>> NumberOfAtoms 26 >> >>>> NumberOfSpecies 2 >> >>>> >> >>>> %block ChemicalSpeciesLabel >> >>>> 1 6 C # Species index, atomic number, species label >> >>>> 2 1 H >> >>>> %endblock ChemicalSpeciesLabel >> >>>> Meshcutoff 200.00 Ry >> >>>> LongOutput T >> >>>> WriteDenchar T >> >>>> AtomicCoordinatesFormat Ang >> >>>> %block AtomicCoordinatesAndAtomicSpecies >> >>>> 0.00 7.37853644 0.000 1 >> >>>> 1.42 7.37853644 0.000 1 >> >>>> -0.71 6.148780367 0.000 1 >> >>>> 2.13 6.148780367 0.000 1 >> >>>> 0.00 4.919024294 0.000 1 >> >>>> 1.42 4.919024294 0.000 1 >> >>>> -0.71 3.68926822 0.000 1 >> >>>> 2.13 3.68926822 0.000 1 >> >>>> 0.00 2.459512147 0.000 1 >> >>>> 1.42 2.459512147 0.000 1 >> >>>> -0.71 1.229756073 0.000 1 >> >>>> 2.13 1.229756073 0.000 1 >> >>>> 0.00 0.00 0.000 1 >> >>>> 1.42 0.00 0.000 1 >> >>>> -0.71 -1.229756073 0.000 1 >> >>>> 2.13 -1.229756073 0.000 1 >> >>>> 0.00 -2.459512147 0.000 1 >> >>>> 1.42 -2.459512147 0.000 1 >> >>>> -0.71 -3.68926822 0.000 1 >> >>>> 2.13 -3.68926822 0.000 1 >> >>>> 0.00 -4.919024294 0.000 1 >> >>>> 1.42 -4.919024294 0.000 1 >> >>>> -0.485 8.218581082 0.000 2 >>>>> -0.485 -5.759068935 0.000 2 >>>>> 1.905 8.218581082 0.000 2 >>>>> 1.905 -5.759068935 0.000 2 >> >>>> %endblock AtomicCoordinatesAndAtomicSpecies >> >>>> >> >>>> %block PAO.BasisSizes >> >>>> C DZP >> >>>> H DZP >> >>>> %endblock PAO.BasisSizes >> >>>> >> >>>> LatticeConstant 2.459512147 Ang >> >>>> %block LatticeVectors >> >>>> 1.732050808 0.00 0.0 >> >>>> 0.0 80.0 0.0 >> >>>> 0.0 0.00 80.0 >> >>>> >> >>>> %endblock LatticeVectors >> >>>> >> >>>> %block BandLines >> >>>> 1 -1.0 0.0 0.0 >> >>>> 40 0.0 0.0 0.0 >> >>>> 40 1.0 0.0 0.0 >> >>>> %endblock BandLines >> >>>> >> >>>> >> >>>> From out-file >> >>>> >> >>>> siesta: Electric dipole (a.u.) = 0.000000 17.412033 >> 0.000000 >> >>>> siesta: Electric dipole (Debye) = 0.000000 44.257004 >> 0.000000 >> >>>> >> >>>> >> >>>> Artem Baskin, >> >>>> PhD student, >> >>>> University of Illinois at Chicago >> >>>> >> >>>> >> >>>> >> >>>> >> >>> >> >>> >> >> >> >> >> >> >> > >> > >> >
