Dear Homa & Fei Those errors are occurring because the script is not able to import other integrated scripts which are located at siesta-3.1/Util/Scripting folder. Now, all you need to do is to check availability of file eggbox_checker.py file in SIESTA's installation directory Example: siesta-3.1/Util/Scripting/eggbox_checker.py. Follow the underlying steps: 1. open terminal go to your file system. Note: replace the following colored lines with the address of *eggbox_checker.py *script file* *which is located under siesta installation directory/Util/Scripting. In this case its siesta-3.1/Util/Scripting/ 2. *chmod +x /home/user/siesta-3.1/Util/Scripting/eggbox_checker.py* 3. */home/user/siesta-3.1/Util/Scripting/eggbox_checker.py PseudoFile.psf [Cutoff] [basis file] *
I hope this will make your work easy...... With Best regards On Mon, Nov 19, 2012 at 8:43 AM, 毛飞 <[email protected]> wrote: > Hi, Ankush**** > > ** ** > > Thank you for your kind reply. I have encountered a problem when I run the > executable eggbox_checker.py.**** > > $ ./eggbox_checker.py H.psf 50 H_dzp.OUT **** > > Where the H_dzp.OUT is the basis file I have produced by gen-basis.sh. The > errors are followed:**** > > ./eggbox_checker.py: line 20: import: command not found**** > > ./eggbox_checker.py: line 21: syntax error near unexpected token > `"$HOME/lib/python/Siesta"'**** > > ./eggbox_checker.py: line 21: `sys.path.append("$HOME/lib/python/Siesta")' > **** > > ** ** > > So, what is the problem and how to fix it? Any comment or suggestion is > appreciated.**** > > ** ** > > Best**** > > Fei Mao**** > > > > > -----原始邮件----- > *发件人:* "Ankush Rai" <[email protected]> > *发送时间:* 2012年11月14日 星期三 > *收件人:* [email protected] > *抄送:* > *主题:* Re: Re: [SIESTA-L] How to fix the eggbox-effect? > > > Hi, > > To run the python script file. Follow the given steps: > 1. open terminal & go to your file system. > 2. Copy the script to your folder. > 3. *chmod +x eggbox_checker.py* > 4. *./eggbox_checker.py PseudoFile.psf [Cutoff] [basis file]* > > Provide the name & values of the parameters such as cutoff & basis > file(without square brackets). This script will make calculation in > temporary folder. Now, plot a graph between Energy v/s Mesh Shift (See > attached file) for each value of cutoff that you will run until relaxation > is acheived. > > ------------------------------------------------------------------------------------------------------------------------------ > 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? > > -------------------------------------------------------------------------------------------------------------------------------- > you shouldn't combine two things at once & there is no relation between > above variables. > > If you intend to use grid cell sampling then use it solitarily & plot the > graph as shown in example to notice the changes. > > Before you perform this steps care should be taken that you must have > already performed sampling for mesh cutoff. > > Ankush > > > > On Tue, Nov 13, 2012 at 2:22 PM, 毛飞 <[email protected]> wrote: > >> Hi, Emilio**** >> >> **** >> >> Actually, I have defined the variable FilterCutoff in my input file, but >> I do not know how to choose the value for it. I just know it should be >> smaller than the value of MeshCutoff (for example, if I choose 400 Ry for >> MeshCutoff, then how about the FilterCutoff).**** >> >> **** >> >> So, the same situation for the variable of FitlerTol, how can I choose a >> value for it. The input and output files are attached in my former email. >> **** >> >> **** >> >> Any comment or suggestion is appreciated. >> >> **** >> >> Best >> >> **** >> >> Fei Mao**** >> >> >> >> >> -----原始邮件----- >> *发件人:* "Emilio Artacho" <[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? >> >> 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 >> >> >> >> >> >
