Dear Fei You could also use filtering (see e.g. FilterTol)
Emilio On 13 Nov 2012, at 11:11, 毛飞 wrote: > Hi, all > > Thank you for your kind reply. I also have learned the script > eggbox_checker.py in the user’s guide, but I do not know how to use it. Can > it be compiled and to be generated as a executable? In the guide, it does not > talk too much about how to use this script, I do not know. And when I obtain > the Fourier components for each species by the script, I have to define the > variable EggboxRemove. > > In addition, you suggested the use of the block of GridCellSampling. So is > there any relationships between these two variables? And do I have to use the > two variables together? > > Any comment or suggestion is appreciated. Thank you in advance. > > Fei Mao > Beijing Normal University, China > > > > -----原始邮件----- > 发件人: "Ankush Rai" <[email protected]> > 发送时间: 2012年11月13日 星期二 > 收件人: [email protected] > 抄送: > 主题: Re: [SIESTA-L] How to fix the eggbox-effect? > > Use the attached script to diagnose the eggbox effect. > You can also use grid sampling. Add following lines to your .fdf file > %block GridCellSampling > 0.5 0.5 0.0 > 0.5 0.0 0.5 > 0.0 0.5 0.5 > %endblock GridCellSampling > care should be taken that grid sampling will need to be modified as per the > system. > I hope it will help. Best regard..... > > > > On Mon, Nov 12, 2012 at 8:24 AM, 毛飞 <[email protected]> wrote: > Hi, all > > Have you ever met the eggbox effect problem before when you do the geometry > optimization with Siesta, and how do you fix it. > > When I optimize the geometry of graphene which is absorbed with a Mg > （Magnesium） atom, I encounter the problem, In my case, the value of Max force > vibrates up and down, which do not go to convergence. I learn to the user’s > guide, it is said that it may fix the problem just by defining the variable > FilterCutoff, but I do not know how to define the suitable value for that > variable (As I know, it should lower than the MeshCutoff. In my case, the > MeshCutoff is 360 Ry, so how about the FilterCutoff? I have attached the > input file and output file). > > Any comment or suggestion is appreciated. Thank you. > > Fei Mao > Beijing Normal University, China > > > > -- Emilio Artacho CIC nanoGUNE Consolider, and Cavendish Laboratory, University of Cambridge Tolosa Hiribidea 76, E-20018 Donostia - San Sebastián, Spain, [email protected], +34 943 574039, http://theory.nanogune.eu
