Dear Fen, as you are using rho2xsf you probably got it along with the whole packed directory, which also contains the README file. It contains some minimal explanations. Looking at your output, I see two problems:
1. Your selected visualization box centered at (1, -2.3, 9) Ang and spanned by three vectors, (1 -3 0.6), (0 8 -2), (-9 0 2) Ang contains no atoms. I don't know why; this was your choice. In case of doubt, try the box coinciding with the Siesta unit cell (centered at 0,0,0 and spanned by three translation vectors); hopefully it will contain some atoms. 2. Your RHO was calculated on a 120*120*120 grid, and, when interpolated onto the 80*80*80 grid used for visualization in XCrySDen, is zero everywhere. This may have two explanations: i) your calculated RHO is zero everywhere as it is calculated (do you have any atoms? see point 1.); ii) your calculation is in the molecular (or slab) mode, and the visualization box is selected very far away from where the atoms are, so that no basis function extends to your visualization box. If you have no idea why, try my suggestion from point 1. Best regards Andrei Postnikov > Dear all > I want to check the charge density about the molecular adsorbed on the > surface. > When we use the rho2xsf , there is a lot of the choices,such like > [...@linux]$ rho2xsf > Specify SystemLabel (or 'siesta' if none): test > Now define the grid cell for your XCrysDen plot. > Note that it can be arbitrarily chosen with respect to the Siesta > simulation cell, and it needs not to be orthogonal. We'll define it by the > origin point and three spanning vectors. They can be given in Bohr or Ang. > Would you use Bohr (B) or Ang (A) ? A > Enter origin point in Ang : 1 -2.3 9 > Enter 1st spanning vector in Ang : 1 -3 0.6 > Enter 2nd spanning vector in Ang : 0 8 -2 > Enter 3rd spanning vector in Ang : -9 0 2 > File Au73-443.XSF exists. Overwrite? (Y/N) > Y > The box contains 0 atoms. > This is OK, just be warned that your XSF file will have no ATOMS secton! > Now define the grid. If you want it two-dimensional, > give 1 as number of grid points along one spanning vector. > Enter number of grid points along three vectors: 80 80 80 > Add grid property (LDOS, RHO, ...; or BYE if none): RHO > Found and opened: Au73-443.RHO > mesh0 = ( 120 120 120 ), nspin= 1 > For is=1: max. grid value = 0.00000E+00 at iix,iiy,iiz= 1 1 1 > For is=1: min. grid value = 0.00000E+00 at iix,iiy,iiz= 1 1 1 > Add grid property (LDOS, RHO, ...; or BYE if none): q > A wild guess! There is no file Au73-443.q; close XSF and quit. > > I can not understand it well, How to set it (in red word), what is this > meaning? > Is there someone can give me tips? > Regards > Fen >
