Dear Artem Thank you for your response.I don't now how they are connected (Or not) I need to find it out.
Best regards Akbar On Fri, Mar 19, 2010 at 11:39 PM, [email protected] <[email protected]> wrote: > 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 > >> >>>> > >> >>>> > >> >>>> > >> >>>> > >> >>> > >> >>> > >> >> > >> >> > >> >> > >> > > >> > > >> > > > > >
