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 100.00 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 > >>>> 0.00 5.889024294 0.000 2 > >>>> 0.00 -5.889024294 0.000 2 > >>>> 1.42 5.889024294 0.000 2 > >>>> 1.42 -5.889024294 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 > >>>> 20 0.0 0.0 0.0 > >>>> 20 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 > >>>> > >>>> > >>>> > >>>> > >>> > >>> > >> > >> > >> > > > > >
