Dear Weslley,
Thank you very much for your attention. Your advice provides me a lot basic understanding on the XSF file. Another SIESTA expert has helped to write a code on reading the charge at each given position. Thank you again. Best wishes! Yours sincerely, Leila 发件人: Weslley Souza Patrocinio [mailto:[email protected]] 发送时间: 2010年9月13日 19:47 收件人: [email protected] 主题: Re: 答复: [SIESTA-L] How to read charge density at a given position? Hi Zhanglei, I tried to work with the rho2xsf code, but I prefered the denchar ones because it is possible to set up more variables. However, when I was looking for XSF informations I found this page: http://www.xcrysden.org/doc/XSF.html#__toc__13 Here is the structure of the XSF grid, which is constructed using the Fortran format, i.e., to access the grid you must to do: C-syntax: for (k=0; k<nz; k++) for (j=0; j<ny; j++) for (i=0; i<nx; i++) printf("%f",value[i][j][k]); FORTRAN syntax: write(*,*) $ (((value(ix,iy,iz),ix=1,nx),iy=1,ny),iz=1,nz) I hope this can help you. Good work, Weslley. On Fri, Sep 10, 2010 at 10:40 PM, zhanglei <[email protected]> wrote: Hi Weslley, Thank you very much for your advice! After reading the manual of Denchar, I found that this code is similar with rho2xsf. I can also define my own XYZ grid and finally obtain a file, named .XSF, with the following format. However, what exactly is the density value for the position, e.g. (2, 0, 0)? # systemLabel.XSF ATOMS 26 4.88240022 -0.08352631 0.00006140 26 6.15692301 2.91460609 0.00000436 … 26 1.84258624 3.60793081 -1.42032133 26 4.99807464 4.87996835 -1.57094524 26 6.09310871 7.32127741 -1.45258353 26 7.95044995 3.67018655 -1.42977940 26 3.70962202 7.27176411 -1.47336896 2 3.66994589 3.47611895 0.00087005 2 4.41715376 2.02051489 -0.00081967 BEGIN_BLOCK_DATAGRID_3D DATA_from:FeHesub.DRHO BEGIN_DATAGRID_3D_DRHO:spin_1 106 112 90 # my definition for grids 1.8000000E+00 -1.0000000E-01 -2.0000000E+00 # for origin 8.0000000E+00 0.0000000E+00 0.0000000E+00 # for origin 0.0000000E+00 8.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 6.0000000E+00 -1.38841E-03 -1.31591E-03 -1.27415E-03 -1.25845E-03 -1.24830E-03 -1.22782E-03 # charge for PIN_UP -1.20458E-03 -1.17644E-03 -1.13945E-03 -1.10145E-03 -1.07345E-03 -1.06778E-03 -1.08766E-03 -1.13587E-03 -1.21489E-03 -1.31853E-03 -1.43500E-03 -1.56127E-03 -1.69482E-03 -1.83016E-03 -1.95622E-03 -2.06447E-03 -2.14878E-03 -2.20475E-03 -2.22827E-03 -2.20652E-03 -2.12539E-03 -1.98227E-03 -1.75469E-03 -1.42163E-03 -9.67779E-04 -3.72732E-04 3.94846E-04 1.36330E-03 2.51582E-03 3.83300E-03 5.24905E-03 6.65572E-03 7.90497E-03 8.81380E-03 9.23699E-03 9.10112E-03 8.42834E-03 7.33264E-03 5.97637E-03 4.52817E-03 3.13710E-03 1.88167E-03 8.06114E-04 -7.24776E-05 -7.47507E-04 -1.26632E-03 -1.65272E-03 -1.93084E-03 -2.11756E-03 -2.22112E-03 -2.26403E-03 -2.24870E-03 -2.19120E-03 -2.10496E-03 -1.99538E-03 -1.86868E-03 -1.73307E-03 -1.59869E-03 -1.47700E-03 -1.37597E-03 -1.28993E-03 -1.23082E-03 -1.18704E-03 -1.15517E-03 -1.11946E-03 -1.08978E-03 -1.05914E-03 -1.01949E-03 -9.65953E-04 -8.96622E-04 -8.17461E-04 -7.38097E-04 -6.44861E-04 -5.87127E-04 -5.82667E-04 -6.33176E-04 -7.40719E-04 -9.09593E-04 -1.12436E-03 -1.36253E-03 -1.59740E-03 -1.80011E-03 -1.92620E-03 -1.91662E-03 -1.75328E-03 -1.39584E-03 -7.76065E-04 1.99780E-04 1.66756E-03 3.85481E-03 7.11264E-03 1.19011E-02 1.87853E-02 2.83026E-02 4.07044E-02 5.55967E-02 7.16452E-02 8.65794E-02 9.76430E-02 1.02481E-01 -1.96892E-03 -1.87333E-03 -1.78008E-03 -1.67960E-03 -1.54126E-03 -1.36418E-03 -1.16541E-03 -9.50314E-04 -7.29789E-04 -5.20021E-04 -3.41712E-04 -2.16724E-04 -1.56353E-04 -1.67128E-04 -2.55162E-04 -4.11668E-04 -6.22298E-04 -8.62564E-04 -1.10974E-03 -1.35241E-03 -1.57851E-03 -1.77418E-03 -1.92991E-03 -2.04025E-03 -2.10153E-03 -2.10917E-03 -2.04315E-03 -1.89085E-03 -1.63939E-03 -1.26519E-03 -7.54049E-04 -7.42874E-05 8.07627E-04 1.92640E-03 3.26230E-03 4.79884E-03 6.47601E-03 8.16225E-03 9.66424E-03 1.07630E-02 1.12784E-02 1.11169E-02 1.03061E-02 8.98425E-03 7.35444E-03 5.62942E-03 3.98765E-03 2.52960E-03 1.29317E-03 2.80759E-04 -4.96747E-04 -1.08476E-03 -1.51833E-03 -1.82481E-03 -2.02718E-03 -2.13098E-03 -2.15088E-03 -2.09996E-03 -1.99896E-03 -1.85410E-03 -1.67151E-03 -1.45910E-03 -1.23033E-03 -1.00228E-03 -7.92862E-04 -6.09925E-04 -4.71887E-04 -3.99387E-04 -3.75643E-04 -4.00874E-04 -4.54887E-04 -5.46884E-04 -6.59238E-04 -7.76363E-04 -8.86315E-04 -9.82501E-04 -1.06423E-03 -1.13222E-03 -1.16198E-03 -1.19549E-03 -1.24500E-03 -1.31885E-03 -1.41988E-03 -1.55406E-03 -1.71279E-03 -1.88134E-03 -2.04065E-03 -2.16515E-03 -2.21541E-03 -2.15413E-03 -1.94014E-03 -1.52900E-03 -8.52978E-04 1.87195E-04 1.73808E-03 4.05135E-03 7.49216E-03 1.25596E-02 1.98610E-02 2.99696E-02 4.31454E-02 5.89619E-02 7.60048E-02 9.18782E-02 1.03677E-01 1.08877E-01 -2.36784E-03 -2.23082E-03 -2.06479E-03 -1.86106E-03 -1.59334E-03 -1.25825E-03 -8.65193E-04 -4.40041E-04 -3.49091E-06 4.15233E-04 7.80971E-04 1.05700E-03 1.21791E-03 1.24918E-03 1.14240E-03 9.11142E-04 5.79221E-04 1.75583E-04 -2.42317E-04 -6.45235E-04 -1.01625E-03 -1.33831E-03 -1.59828E-03 -1.78929E-03 -1.90850E-03 -1.95382E-03 -1.91890E-03 -1.77110E-03 … Thank you very much! Best wishes! Yours sincerely, Leila 发件人: [email protected] [mailto:[email protected]] 代表 Weslley Souza Patrocinio 发送时间: 2010年9月10日 19:53 收件人: [email protected] 主题: Re: [SIESTA-L] How to read charge density at a given position? Hi, Leila. You can use the Denchar (one of the Siesta utils) to generate the charge density distribution. In the input file of you will define the region in the space that you want to calculate the charge density and the number of discretization points, so you can build your own XYZ grid and choose the points that are important. Good luck! Yours, Weslley. -- Weslley Souza Patrocinio Pesquisador Departamento de Nanotecnologia Centro de Pesquisas Avançadas Wernher von Braun e-mail: [email protected] skype: weslley.vonbraun -- Weslley Souza Patrocinio Pesquisador Departamento de Nanotecnologia Centro de Pesquisas Avançadas Wernher von Braun e-mail: [email protected] skype: weslley.vonbraun
