Thank you for your kind reply. Would you please have a look at my newly modified input file (attached) for optimization graphene, if there is anything wrong, you could tell me and give some advice on how to fix it.
And you mentioned a recent message also referenced graphene that I have not found (I want go to find it in website of the Mail Archive, but it can not be opened), so could you send me the message (mainly the input file) in e-mail. Thank you in advance. Any comment or suggestion is appreciated. Best Fei Mao -----原始邮件----- 发件人: "Abraham Hmiel" <[email protected]> 发送时间: 2012年11月8日 星期四 收件人: [email protected] 抄送: 主题: Re: Re: [SIESTA-L] Problem of graphene sheet optimization The unit cell you have defined in your input file you just sent cannot b right. Think about it- you are defining a simulation cell with dimensions LatticeConstant 2.46 Ang %block LatticeVectors 0.866 0.5 0.000 -0.866 0.5 0.000 0.0 0.0 1.0 %endblock LatticeVectors that means the basis functions of all your atoms will be overlapping in the z-direction since they will be 2.46 Angstroms away from each other! You need to increase the size of the z-dimension of your unit cell to at least 12 Angstroms to avoid atom-image interactions. Specifically, the z-dimension for a 2D material should be more than double the longest basis set cutoff radius. Additionally, you have defined atomic coordinates that are greater than your lattice vectors in the xy-directions. That means they will be translated back onto the unit cell you've defined. This cell you've defined looks like it might be good for a 2-atom cell, but you've got 54 atoms packed into it, so it's no wonder why your simulation isn't converging! There was another message on the list very recently that referenced graphene. That individual had another issue with his output, but (s)he had defined the unit cell correctly. Maybe take a look at that for starters. After you figure out what simulation cell and atomic coordinates to use, you should optimize the lattice constant using the MD.VariableCell .true. keyword- The cell size will be slightly different for different basis set sizes and XC-functionals. If you want to find the global minimum in the potential energy surface, you need to allow the cell size to relax, using the experimental lattice constant as a starting point. The converged cell vectors should not differ by more than 2-4% or so compared to the experimental ones. You also need to make sure the k-point sampling is very dense around the K points of the Brillouin zone, since graphene is a semimetal and the bands cross the Fermi Level at a single point. Use at least a 30x30x1 Monkhorst-Pack k-point mesh. Best, On Thu, Nov 8, 2012 at 9:36 AM, 毛飞 <[email protected]> wrote: Hi, Heiko Dumlich Thank you for your kind reply. I have modified the input file for Siesta, and it is attached. I am testing the input file if it works. I have two questions. a) Because graphene is a 2D material, I just want to know whether the unit cell defined in the input file is right or not? b) The variable LatticeConstant is set by an experimental value. Maybe when I have successfully optimized the geometry, the LatticeConstant is changed, then I should set which one to be the LatticeConstant, the experimental one, or the optimized one? Any comment or suggestion is appreciated. Best Fei Mao -----原始邮件----- 发件人: "Heiko Dumlich" <[email protected]> 发送时间: 2012年11月8日 星期四 收件人:[email protected] 抄送: 主题: Re: [SIESTA-L] Problem of graphene sheet optimization Dear Fei Mao, your unit cell does not periodically repeat the graphene structure. Further none of your calculations is converged. You should think about your unit cell LatticeConstant 2.44 Ang %block LatticeVectors 13.000 0.000 0.000 0.000 13.000 0.000 0.000 0.000 4.100 %endblock LatticeVectors and optimize the values to create an infinite graphene sheet. Then the optimization becomes far less demanding, as no dangling bonds exist at the edge. If you desire dangling bonds at the edge, you have to at least converge your calculations to a decent value, which "siesta: 99 -8321.6798 -8318.5587 -8318.5639 0.9802 -4.8893" definitely is not true for dDmax=0.9802. Good Luck Heiko Dumlich On 11/08/2012 09:50 AM, 毛飞 wrote: Hi, all Has anyone ever tried to get a well converged geometry optimization of pure graphene, which is not passivated with any hydrogen atoms in the edge of graphene layer. In that case, the carbon atoms in the edge of graphene are kept with dangling bonds. I have done this job within many codes, and all failed. I find it is very hard to do this, but in many published scientific papers, there are the energy band analysis of pure graphene (and sometimes adsorbed with adatom), such as DOS, or PDOS. It is very amazing, it seems that these authors have the pure graphene relaxed fully. Or they obtain the band structure with not fully relaxed graphene sheet. Do you have any ideas? I attach the input and output files for optimizing the pure graphene by using Siesta codes (in order to obtain the converged geometry optimization, I have increased the MeshCutoff to 400 Ry, it still does not work). Any comment or suggestion is appreciated. Thank you. Fei Mao Beijing Normal University -- Heiko Dumlich Freie Universität Berlin Fachbereich Physik - AG Reich Arnimallee 14 D-14195 Berlin GERMANY Phone: +49-30-838 56157 -- Abraham Hmiel Katherine Belz Groves Fellow in Nanoscience Xue Group, College of Nanoscale Science and Engineering at SUNY Albany http://abehmiel.net/about
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