> Andrei, > > thank you very much for your answer. I had already found in the ML > database > the nice phonon reference you indicated to me. > By negative frequencies, I mean: > > eigenvalue # 1 omega= -40.738952961112830 > eigenvalue # 2 omega= -2.05736482791876937E-002 > eigenvalue # 3 omega= -1.32180970904245670E-002
Dear Carlo, Your frequencies 2 and 3 are zero, for all practical use. No special importance therefore that they are negative. If you have yet the third frequency (positive, in your case?) which is as close to zero as those two (your Nr4?) then likely you don't have a problem with MeshCutoff. However, your frequency Nr1 is an indication that your relaxation is not good enough. The negative frequency (if a stable one and not due to numerical noise) means: as you displace the atoms in some combination, the energy goes down. It shouldn't be like this at the equilibrium. Have a look into p.18 of http://www.home.uni-osnabrueck.de/apostnik/Lectures/APostnikov-Phonons.pdf > My system is a molecular junction. Just to explain you, at the beginning I > calculated the electrodes bulk lattice parameter, and then I built the > junction geometry. If I then relax by setting MD.variableCell=T the cell > dimensions increase by 1.5%... Do you think that I should necessarily use > a variable cell in the relaxation? (I am suspicious about it) Not necessarily at all; you can calculate phonons in a constrained system, under pressure etc. However, atom positions have to be optimized subject to this constraint (to be sure that trial atom displacements are around the equilibrium). > Finally, could you please give me some reference about the eggbox effect > test? It has been discussed many many times in the main list and in tutorials. E.g., you may have a look in http://www.home.uni-osnabrueck.de/apostnik/Lectures/SIESTA-tuto.pdf (pp.10-12) Good luck Andrei Postnikov > > Thank you very much! > > Carlo > > > 2012/4/7 <[email protected]> > >> Dear Carlo, >> as you don't specify how negative your negative frequencies are, >> it is not so easy to judge... Your sum of forces seems a bit too high... >> Even if not dramatically... And some individual forces as well - >> e.g., Fx on atom 2. So generally I'd recommend even higher MeshCutoff >> and further relaxation. A priori 350 Ry is not safely high, >> sometimes one needs to go to much higher. >> >> Before doing the phonons, I'd recommend the usual "eggbox test" >> to be sure that fluctuations of summary force as function of >> uniform displacement of all atoms remain within |0.1|. >> >> Concerning specifically the phonons, you may wish to check >> http://www.home.uni-osnabrueck.de/apostnik/Lectures/APostnikov-Phonons.pdf >> - especially p.18 of it. >> >> Best regards >> >> Andrei Postnikov >> >> >> > Dear Siesta users, >> > >> > I am trying to calculate phonon frequencies at Gamma for a molecular >> > junction. >> > I relaxed the system by keeping fixed the Lattice Vectors (not a >> variable >> > cell). When I compute the frequencies (with MeshCutoff = 200 Ry), I >> obtain >> > that the first three frequencies are negative, which indicates that >> the >> > results are not correct. >> > Then, if I increase the MeshCutoff to 350 Ry (which seems a high value >> to >> > me) I obtain again negative frequencies. >> > Could you suggest me how to fix the problem? >> > The following are the forces of the system...do you think that they >> are >> > too >> > high? Which is a good criteria to say that the forces are low enough? >> > >> > Thank you very much, >> > >> > Carlo >> > >> > siesta: 1 0.106233 -0.096180 0.047641 >> > siesta: 2 -0.655838 0.034936 -0.004086 >> > siesta: 3 0.364736 -0.100368 0.166114 >> > siesta: 4 0.130690 0.010500 -0.101584 >> > siesta: 5 -0.122410 0.420815 -0.012044 >> > siesta: 6 0.120625 -0.031292 0.152270 >> > siesta: 7 0.003319 0.004051 -0.012274 >> > siesta: 8 0.004951 -0.015719 0.001451 >> > siesta: 9 -0.009523 0.004610 0.013162 >> > siesta: 10 0.019411 -0.008606 -0.009840 >> > siesta: 11 0.002485 -0.010131 0.005577 >> > siesta: 12 0.001815 -0.012882 -0.010601 >> > siesta: 13 0.002293 -0.027828 0.004317 >> > siesta: 14 0.003541 -0.004099 -0.003595 >> > siesta: 15 -0.004545 -0.005597 0.018501 >> > siesta: 16 -0.002375 0.005693 -0.016887 >> > siesta: 17 0.007410 -0.017539 -0.001118 >> > siesta: 18 0.015827 -0.012960 -0.005705 >> > siesta: 19 -0.010629 -0.007460 -0.001509 >> > siesta: 20 0.008748 0.000683 -0.004698 >> > siesta: 21 -0.004943 0.029703 -0.008064 >> > siesta: 22 -0.003202 0.004500 0.030359 >> > siesta: 23 -0.009982 -0.003884 -0.044988 >> > siesta: 24 0.012110 -0.008463 -0.054600 >> > siesta: 25 0.014891 0.000114 0.030375 >> > siesta: 26 0.011714 0.007854 -0.002981 >> > siesta: 27 -0.006905 -0.024651 0.005841 >> > siesta: 28 0.002399 -0.019318 0.013282 >> > siesta: 29 -0.019852 0.006114 -0.030653 >> > siesta: 30 -0.023687 0.004007 -0.028044 >> > siesta: 31 0.023195 -0.022556 -0.014991 >> > siesta: 32 0.024333 -0.033430 -0.028258 >> > siesta: 33 -0.014937 0.006378 0.009843 >> > siesta: 34 0.004912 -0.019004 -0.008074 >> > siesta: 35 0.006259 -0.012323 0.009612 >> > siesta: 36 -0.010453 0.017222 0.013853 >> > siesta: 37 0.001281 0.001284 -0.002971 >> > siesta: 38 0.009564 0.017869 -0.013170 >> > siesta: 39 0.004626 -0.016715 -0.008634 >> > siesta: 40 0.008447 -0.028871 -0.007756 >> > siesta: 41 -0.020042 -0.027721 -0.021694 >> > siesta: 42 0.020027 -0.019833 -0.095505 >> > siesta: ---------------------------------------- >> > siesta: Tot 0.016519 -0.011098 -0.032128 >> > >> > >> > -- >> > >> > Carlo Motta >> > * Ph.D. Student in Materials Science* >> > University Office Phone : +39 02 6448-5183 >> > Department of Materials Science >> > University of Milano-Bicocca >> > Via R. Cozzi 53, 20125 Milano, Italy >> > >> >> >
