Hamidreza, I'd like to help you solve your problem, but it seems like you have not read the manual to learn how to perform a proper calculation. Please do so. Additionally, if you search the mailing list archives, you will find working graphene input .fdf files that yield plausible results because this question has been asked dozens of times. For example: http://www.mail-archive.com/[email protected]/msg02155.html
Here is what comes to mind when I read your input file: 1. Why are you using siesta 2.0.2? The most recent version is profoundly better and has more features. Unless there is a specific reason to use 2.0.2, you should upgrade to the new version. 2. For an infinite graphene sheet, 10x10x1 M-P k-point grid is not good enough because it is too coarse around graphene's dirac points in the BZ. You will need at least 48x48x1 from experience. 3. 20 Ry is way too small for the MeshCutoff. Try at least 10 times this value, and you will need to converge this value with respect to total energy. 4. (The reason why your simulation is not working) you have no atoms listed inside your "AtomicCoordinatesAndAtomicSpecies" block. If you have no species listed here, I believe the program will make the coordinates of everything (0,0,0), hence why it prints that warning that specific atoms are too close together. Finally, when attaching items in an email to the list, please use plain text (or .png for figures) from now on. I'm also not sure why you posted your message five times to the list, it is mildly irritating to see such a thing in my inbox and might make people less willing to help you. Hope this helps and good luck with your calculation, -- *Abraham Hmiel* Katherine Belz Groves Fellow in Nanoscience Xue Group, College of Nanoscale Science and Engineering at SUNY Albany http://abehmiel.net/about
