> Dear Mehmet, > I used your input values but I still get a negative part in the curve. I > tried re doing the calculation with LDA pseudo. For LDA there is no > negative > part whereas GGA (PBE) gives me negative part. > Could someone comment on why this should happen for different pseudos.
Dear Juzar, I can suggest a small checklist to get to the bottom of your problem. Forget the pseudos for the moment, they are not your principal worry. 1. Do you have, among Gamma-modes, three good acoustic ones, with frequencies close enough to zero? - if not, the problem is insufficient MeshCutoff. 2. Are other frequencies at Gamma positive? - if not, you are calculating phonons not around the equilibrium (this might be intentional, of course, in some cases). Go search for a better equilibrium. Use eigenvectors of instable modes as a guide. 3. If Gamma modes are OK but negative modes appear someplace along the dispersion curves. This can be, in principle, either genuine (a true instability - but needs careful checking!), but more often is due to insufficient supercell size in vibra calculations. I understand that this behaviour may vary with pseudopotential, but in a collateral and random way; k-mesh and MeshCutoff convergencies are much more important. You can go through checklist and enforce stable phonons with any pseudopotential. (The values of stable modes is a different issue). Good luck Andrei Postnikov > dont think there is a problem with the pseudo because it is well tested > for > other calculations.) > > Regards, > > Juzar Thingna > Department of Physics, > Center for Computation Science and Engineering, > National University of Singapore. > > > On Mon, Jul 26, 2010 at 9:42 PM, Mehmet Topsakal < > topsa...@unam.bilkent.edu.tr> wrote: > >> Dear Jusar, >> >> Your structure in C2.fdf does not look like 2D-graphene. >> >> Try these >> >> >> NumberOfSpecies 1 >> NumberOfAtoms 2 >> LatticeConstant 1.0007 Ang >> %block LatticeVectors >> 2.4644 0 0 >> 1.2322 2.13423302 0 >> 0 0 10 >> %endblock LatticeVectors >> >> AtomicCoordinatesFormat fractional >> %block AtomicCoordinatesAndAtomicSpecies >> 0.33333333 0.33333333 0.5 1 >> 0.66666666 0.66666666 0.5 1 >> %endblock AtomicCoordinatesAndAtomicSpecies >> >> >> Also the attached pdf is the phonon-spectrum that i calculated by using >> phon >> (http://www.homepages.ucl.ac.uk/~ucfbdxa/phon/<http://www.homepages.ucl.ac.uk/%7Eucfbdxa/phon/> >> ) >> >> On Mon, Jul 26, 2010 at 1:41 PM, Juzar Thingna <juza...@gmail.com> >> wrote: >> >>> Hello Everyone, >>> >>> I'm trying to calculate the phonon dispersion relation of graphene >>> sheet. >>> In this calculation I get negative frequencies. Please could someone >>> guide >>> me where I'm going wrong? >>> >>> These are my input files: >>> 1) C2.fdf >>> >>> SystemName graphene >>> SystemLabel C2 >>> >>> NumberOfAtoms 2 >>> LatticeConstant 2.46 Ang >>> >>> %block LatticeVectors >>> 0.86 -0.5 0.0 >>> 0.86 0.5 0.0 >>> 0.0 0.0 20.0 >>> %endblock LatticeVectors >>> >>> AtomicCoordinatesFormat NotScaledCartesianAng >>> %block AtomicCoordinatesAndAtomicSpecies >>> 0.0 0.0 0.0 1 12.0 >>> 1.42 0.0 0.0 1 12.0 >>> %endblock AtomicCoordinatesAndAtomicSpecies >>> >>> SuperCell_1 3 >>> SuperCell_2 3 >>> >>> AtomicDispl 0.04 Bohr >>> >>> BandLinesScale ReciprocalLatticeVectors >>> %block BandLines >>> 1 0.000 0.000 0.000 \Gamma >>> 20 0.500 0.000 0.000 M >>> 20 0.333 -0.333 0.000 K >>> 20 0.000 0.000 0.000 \Gamma >>> %endblock BandLines >>> >>> 2) C2-siesta.fdf >>> >>> # graphene, 2 C in each unit cell >>> # optimize structure(15/06/10/Tue) >>> # cal. FC(16/06/10/Wed) >>> # use ./vibrator to calculate phonon(16/06/10/Wed) >>> >>> SystemName graphene >>> SystemLabel C2 >>> >>> NumberOfSpecies 1 >>> %block ChemicalSpeciesLabel >>> 1 6 C >>> %endblock ChemicalSpeciesLabel >>> >>> PAO.BasisSize DZP >>> XC.functional GGA >>> XC.authors PBE >>> >>> MeshCutoff 200.0 Ry >>> DM.MixingWeight 0.3 >>> DM.NumberPulay 3 >>> DM.Tolerance 1.0d-5 >>> >>> %include FC.fdf >>> >>> First I run the utility fcbuild followed by siesta and then the utility >>> vibrator to get the spectrum. >>> >>> Regards, >>> >>> Juzar Thingna >>> Department of Physics, >>> Center for Computation Science and Engineering, >>> National University of Singapore. >>> >> >> >> >> -- >> >> Mehmet Topsakal (Ph.D. Student) >> UNAM-Institute of Materials Science and Nanotechnology. >> Bilkent University. 06800 Bilkent, Ankara/Türkiye >> Tel: 0090 312 290 3527 ; Fax: 0090 312 266 4365 >> UNAM-web : www.nano.org.tr >> >> >
