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 >>>> >>>> >>>> >>>> >>> >>> >> >> >> > >
