[SIESTA-L] plotting difficulty
Dear all, I know this is not directly related to siesta, but I really need you to share your experience with me. I have managed to plot my graphs with xmgrace. But I am not quite familiar with the setting of my data on the graphs. Do you have any idea of how to : 1. set the fermi level to zero in the graphs? 2. Would you please let me know how I can limit the y-axis ? 3. How I can put the high symmetry point group labels on the x-axis. 4. Finally, How can I present two seperate files in one graph with xmgrace. Please do forgive me for these questions, I am really at loss no one around me has no idea of how to work with grace!!! Regards, Catrina
[SIESTA-L] plotting band-structure
Hi everyone, I am sorry that this question may be so wierd. I have tried to plot the band structure by gnuplot but whatever I did the high symmetry points are not being mentioned correctly. I have tried so much, but I could not manage to do it. Is it possible that I have the script you use for plotting the band structure by gnuplot? Regards, Catrina
[SIESTA-L] Polarization grid
Dear all, In my calculations on the nanowires, I have used the polarization grid to calculate the LO-TO splittings in the wires. But, it seems that I have problem arranging the digits in the polarization grid. The grid I have used is as follows: %block PolarizationGrids 8 1 1 no 8 8 1 no 1 1 16 yes %endblock PolarizationGrids BornCharge True I have got wrong results. Please let me know if I can solve this problem. Regards, Catrina
[SIESTA-L] electric field theory
Hi, I want to know that by applying the electric field in siesta, we are calculating the response of the system to electric field perturbation through DFPT? Please let me know what theory does siesta follw in appying the external electric field. regards, Catrina
Re: [SIESTA-L] passivation unconverged
I decreased the mixingweight to 0.02 and I got converged. But could you kindly let me know how you optimize the "c" parameter of the wires? I have my own method, but seems to me unreliable, although for unstaurated one I have got good results. Regards, Catrina From: Danil Boukhvalov To: SIESTA-L@listserv.uam.es Sent: Friday, January 2, 2009 1:07:39 AM Subject: Re: [SIESTA-L] passivation unconverged Hello Catrina, in similar cases I decrese mixweight to 0.03~0.02 or less, and increase number of SCF itterations. For several model nanostructures it work. > Hello all, > > I have ran siesta for different diameters of bare nanowires of zinc oxide, > well converged and good results achieved. > > But Now I have passivated the wires and I have put the bond length of H-Zinc > and H-Oxygen as 1.55 and 0.98 Angstrom respectively. But I could not > converge the scf cycles even by putting mixingweight as 0.05. > > Please let me know what I should do to correct my passivation. > > Regards, > Catrina > > > >
[SIESTA-L] passivation unconverged
Hello all, I have ran siesta for different diameters of bare nanowires of zinc oxide, well converged and good results achieved. But Now I have passivated the wires and I have put the bond length of H-Zinc and H-Oxygen as 1.55 and 0.98 Angstrom respectively. But I could not converge the scf cycles even by putting mixingweight as 0.05. Please let me know what I should do to correct my passivation. Regards, Catrina
[SIESTA-L] problem with pdosxml
Dear all, Happy 2009. I have calculated the PDOS in the files I have converged and now I want to plot DOS for different orbitals. I saw the files: m_orbital_chooser.f90, m_pdos.f90 and pdos.f90 in the UTIL, also in the mailing list I saw a fortran file for plotting the DOS ?!?! Please let me know which one i should compile and which one I should use to change it to gnuplot format? Regards, Catrina
[SIESTA-L] H-passivation
Hi, Does anybody have the experience of saturating the dangling bonds with hydrogen? how can we have the coordinates of "H" atoms? Regards, Catrina
Re: [SIESTA-L] [SUSPECTED-SPAM] Re: [SIESTA-L] ./optical
Hello, can you run the regular "siesta" (compiled with gfortran) ? yes I can. I also do not receive segfaults while I compile other .f files in utility, this has occured only for "optical" what should I change in it to get the run? Regards, Catrina From: Sushil Auluck <[EMAIL PROTECTED]> To: SIESTA-L@listserv.uam.es Sent: Sunday, December 7, 2008 12:50:24 PM Subject: Re: [SIESTA-L] [SUSPECTED-SPAM] Re: [SIESTA-L] ./optical http://www.iitk.ac.in/phy/People/phy_facvis.html http://www.iitk.ac.in/phy/New01/profile_SA.html
Re: [SIESTA-L] ./optical
To respected siesta users, when I run input using ./input < SysLabel.EPSIMG and then I write ./optical without the arrow, still the segmentation fault occurs ?!?! What is the reason? Regards, Catrina From: Marty Blaber <[EMAIL PROTECTED]> To: SIESTA-L@listserv.uam.es Sent: Sunday, December 7, 2008 9:31:38 AM Subject: Re: [SIESTA-L] ./optical To all respected siesta users, I have compiled siesta with gfortran. After compiling optical from "utility" when I write ./optical
[SIESTA-L] ./optical
To all respected siesta users, I have compiled siesta with gfortran. After compiling optical from "utility" when I write ./optical
Re: [SIESTA-L] URGENT (supercell for bulk)
To all respected siesta users, Thank you very much for helping me. I have used the usual way (not supercell) for hexagonal system of mine, using the method mostly discussed here in mailing list. In the .out file of variable cell, I have "Naive supercell factors: 885". The result I have got is that the "a" parameter is about 2% less than the experimental value and "c" parameter is about 3% more than the experimental value. Reading the article, it came to my mind maybe I can change the "Naive supercell factors" at the same time "superc: Internal auxiliary supercell" in order to change the interactions in a way to have the parameters change in the same manner (I mean they all decrease or increase). Therefore, I changed some parameters and the final result was "Naive supercell factors: 6 64", I could not get to "6 6 2". The result was that I got "c" 0.5% more than experiment, but "a" changed only slightly from the previous result. I want to know is what they mean of supercell is what I have understood? and if it is 'yes' how I can change the parameters to get to it? does it really enhance the job? Regards, Catrina From: Yurko Natanzon <[EMAIL PROTECTED]> To: SIESTA-L@listserv.uam.es Sent: Tuesday, November 25, 2008 8:19:21 PM Subject: Re: [SIESTA-L] URGENT (supercell for bulk) Dear Catrina, Mind that you have periodical boundary conditions so your unit cell is repeated infinite number of times in all directions. So, you only need to construct a supercell if you want to break the symmetry (i.e. introduce defects). Or if you want to imitate zero boundary conditions (i.e. for isolated molecules, surfaces etc) by constructing a large supercell with a vacuum layer. if you calculate just an ideal bulk crystal, making supercell does not change anything at all because of periodic boundary conditions! so you just waste the computation time if you do it. regards, Yurko 2008/11/25 catrina desport <[EMAIL PROTECTED]>: > Dear Andrei Postnikov, > > I am sorry if my words were confusing. Actually, it is not the matter of > imitating at all. I just wanted to know if having supercell for some systems > like bulk hexagonal helps to get better answers. > > I didn't enclose their article to keep it from judgements, but in a > presentation I found from the work they did, I saw the below lines: > > Bulk ... (hexagonal system) > SIESTA: TM pseudopotential, ... basis, ... Ry mesh cutoff, LDA > Piezoelectric constant > Berry Phase: e33=... C/m2 > Our O(N) method: e33=... C/m2 > 6×6×2 supercell > > Again, I insist, it is not the matter of imitating at all, just wanted to > know if there's a helpful method to get reasonable parameters for hexagonal > systems, especially those which are abit unstable. > > I hope to have your valuable response. > Regards, > Catrina > > From: "[EMAIL PROTECTED]" <[EMAIL PROTECTED]> > To: SIESTA-L@listserv.uam.es > Sent: Tuesday, November 25, 2008 6:32:02 PM > Subject: Re: [SIESTA-L] URGENT (supercell for bulk) > >> To all respected siesta users: >> >> Considering >> an article on a hexagonal lattice, written by authors who have worked >> with siesta, I have encountered that they have used 6x6x2 supercell for >> their "bulk" system !!! > > Dear Catrina: > if it is really supercell used in their calculation and not just > superc: Internal auxiliary supercell > message, then they should have had a good reason for doing it > (usually, modeling a point defect, ) and not just bulk? > >> I need to know how they have done it to >> generate the appropriate supercell > > I'd guess, rather by hand or by using the SuperCell block > (once, and then exporting the generated coordinates in the input file) > >> for better optimization for my >> system as well.. > > I wonder how can supercell help in "better optimization of your system"? > >> Please do guide me, it is very urgent for me. > > This is difficult for two reasons: > you do not explain what you want to do, > and refer to other peoples' work which you apparently want to imitate, > without giving any details or reference. > > Best regards > > Andrei Postnikov > > -- Yurko (aka Yuriy, Iurii, Jurij etc) Natanzon PhD Student Henryk Niewodniczan`ski Institute of Nuclear Physics Polish Academy of Sciences ul. Radzikowskiego 152, 31-342 Krako`w, Poland Email: [EMAIL PROTECTED], [EMAIL PROTECTED]
Re: [SIESTA-L] URGENT (supercell for bulk)
Dear Andrei Postnikov, I am sorry if my words were confusing. Actually, it is not the matter of imitating at all. I just wanted to know if having supercell for some systems like bulk hexagonal helps to get better answers. I didn't enclose their article to keep it from judgements, but in a presentation I found from the work they did, I saw the below lines: Bulk ... (hexagonal system) SIESTA: TM pseudopotential, ... basis, Ry mesh cutoff, LDA Piezoelectric constant Berry Phase: e33=... C/m2 Our O(N) method: e33=... C/m2 6×6×2 supercell Again, I insist, it is not the matter of imitating at all, just wanted to know if there's a helpful method to get reasonable parameters for hexagonal systems, especially those which are abit unstable. I hope to have your valuable response. Regards, Catrina From: "[EMAIL PROTECTED]" <[EMAIL PROTECTED]> To: SIESTA-L@listserv.uam.es Sent: Tuesday, November 25, 2008 6:32:02 PM Subject: Re: [SIESTA-L] URGENT (supercell for bulk) > To all respected siesta users: > > Considering > an article on a hexagonal lattice, written by authors who have worked > with siesta, I have encountered that they have used 6x6x2 supercell for > their "bulk" system !!! Dear Catrina: if it is really supercell used in their calculation and not just superc: Internal auxiliary supercell message, then they should have had a good reason for doing it (usually, modeling a point defect, ...) and not just bulk? > I need to know how they have done it to > generate the appropriate supercell I'd guess, rather by hand or by using the SuperCell block (once, and then exporting the generated coordinates in the input file) > for better optimization for my > system as well. I wonder how can supercell help in "better optimization of your system"? > Please do guide me, it is very urgent for me. This is difficult for two reasons: you do not explain what you want to do, and refer to other peoples' work which you apparently want to imitate, without giving any details or reference. Best regards Andrei Postnikov
[SIESTA-L] URGENT (supercell for bulk)
To all respected siesta users: Considering an article on a hexagonal lattice, written by authors who have worked with siesta, I have encountered that they have used 6x6x2 supercell for their "bulk" system !!! I need to know how they have done it to generate the appropriate supercell for better optimization for my system as well. Please do guide me, it is very urgent for me. Best regards, Catrina
